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<h3>
Aaron M. Ucko pushed to branch master
at <a href="https://salsa.debian.org/med-team/sra-sdk">Debian Med / sra-sdk</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/16b194b3db9acbdba0ed4f80dc444cd0dacb9d2f">16b194b3</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:46:16-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/6461e62e68fb5d8dcde3de71bb531257330decb2">6461e62e</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:46:22-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.10.7+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/8c214ea2471d1dd0c5f5b0c3307bfab757cdf5b7">8c214ea2</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:46:43-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/2.10.7+dfsg'
Upstream version 2.10.7+dfsg
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/05d30486bbe4b46c592ead2bf94d0a513bb8d06b">05d30486</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:47:29-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes: lintian: file-contains-trailing-whitespace
See-also: https://lintian.debian.org/tags/file-contains-trailing-whitespace.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/07f2e1388c548cb50f273fe8fa1586c69baab613">07f2e138</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:47:32-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set field Upstream-Contact in debian/copyright.</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/97ee260c30cb91208f195775419c129640f2ca99">97ee260c</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:47:37-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
Fixes: lintian: upstream-metadata-missing-repository
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-repository.html
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/305ea939baaa7df1cfbea57e4ddf18eb273e9e1d">305ea939</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T21:47:38-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove obsolete field Contact from debian/upstream/metadata (already present in machine-readable debian/copyright).</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/f80fa3d29c2187f911563e3ed3be939a53d58d60">f80fa3d2</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2020-06-02T22:04:35-04:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>28 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#c9512c0b1798e84b5d6a945ad880784dab140a53">
build/Makefile.vers
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<li class="file-stats">
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build/docker/Dockerfile.build-alpine
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<li class="file-stats">
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build/docker/Dockerfile.build-amazonlinux
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build/docker/Dockerfile.build-ubuntu
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build/docker/Dockerfile.delite
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/copyright
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debian/rules
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debian/upstream/metadata
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shared/toolkit.vers
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<a href="#5cd76f234790117309267153be422c6d4e826541">
shared/toolkit.vers.h
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<a href="#b3f7be8d2cddbea73a24a16a7011a3dce42fa650">
test/driver-tool/Makefile
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tools/driver-tool/imp_fasterq_dump.cpp
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<a href="#e7acf3882da8bde42f6b4ae537f55850c8352c0e">
tools/driver-tool/proc.posix.cpp
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tools/driver-tool/proc.win32.cpp
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tools/driver-tool/run-source.cpp
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tools/driver-tool/util.hpp
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tools/kar/DL/UPD.sh
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tools/kar/README.txt
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tools/kar/delite_docker.sh
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tools/kar/sra_delite.kfg
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<a href="#a84cd173c686120c42e6d4c9296132e65c8cb7db">
tools/kar/sra_delite.sh
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># NCBI External Developer Release:</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.10.7</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**May 20, 2020**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"> <span class="gs" style="font-weight: 600;">**sratools**</span>: fixed issue with some runs not working correctly and fixed typo in fasterq-dump command line</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SRA Toolkit 2.10.6</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**MAY 18, 2020**</span></span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#c9512c0b1798e84b5d6a945ad880784dab140a53"><strong>build/Makefile.vers</strong></a>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># ===========================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># SRA-TOOLS and library version</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.10.<span class="idiff left right">6</span></span></pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 2.10.<span class="idiff left right">7</span></span></pre>
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<li id="f2eba9c79ef445c608c5970aef78ace393fe70b1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#f2eba9c79ef445c608c5970aef78ace393fe70b1"><strong>build/docker/Dockerfile.build-alpine</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">FROM alpine:latest AS build-base</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RUN apk add build-base util-linux linux-headers g++ bash perl make cmake git bison flex</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">FROM build-base AS build</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ARG VDB_BRANCH=master</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ARG NGS_BRANCH=${VDB_BRANCH}</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ARG SRA_BRANCH=${VDB_BRANCH}</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ARG BUILD_STYLE=--without-debug</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">RUN git clone -b ${NGS_BRANCH} --depth 1 https://github.com/ncbi/ngs.git</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">RUN git clone -b ${VDB_BRANCH} --depth 1 https://github.com/ncbi/ncbi-vdb.git</span>
</pre>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">RUN git clone -b ${SRA_BRANCH} --depth 1 https://github.com/ncbi/sra-tools.git</span>
</pre>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">WORKDIR /ncbi-vdb</span>
</pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">RUN sed -e '/gnu\/libc-version.h/ s/^/\/\//' -e '/gnu_get_libc_version/s/^/\/\//' -i libs/kns/manager.c</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">WORKDIR /ngs</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s -C ngs-sdk >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">WORKDIR /sra-tools</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">RUN sed -e'/execinfo.h/ s/^/\/\//' -e'/backtrace/ s/^/\/\//' -i tools/driver-tool/secure/except.cpp</span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">RUN sed -e'/mv -b -v/ s/mv -b/mv/' -i build/install-kfg.sh</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">RUN perl -pi.orig -e'BEGIN{@l=(279,383,407,415,416,420,770,907);$i=0}if ($.==$l[$i]){++$i;s/stdout/use_stdout/g unless /use_stdout/}' tools/fasterq-dump/fasterq-dump.c && rm -f tools/fasterq-dump/fasterq-dump.c.orig</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">RUN make install</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">RUN mkdir -p /root/.ncbi</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">RUN printf '/LIBS/GUID = "%s"\n' `uuidgen` > /root/.ncbi/user-settings.mkfg</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"># SEND CLOUD INSTANCE IDENTITY</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">RUN printf '/libs/cloud/report_instance_identity = "true"\n' >> /root/.ncbi/user-settings.mkfg</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">FROM alpine:latest</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">LABEL author="Kenneth Durbrow" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> maintainer="kenneth.durbrow@nih.gov" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> vendor="gov.nih.nlm.ncbi" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> website="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> repository="https://github.com/ncbi/sra-tools/" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> description="The SRA Toolkit along with a working default configuration." \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> NOTICE="WHEN USING THIS IMAGE IN A CLOUD ENVIRONMENT, YOU WILL BE SENDING YOUR CLOUD INSTANCE IDENTITY TO NCBI."</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">COPY --from=build /etc/ncbi /etc/ncbi</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">COPY --from=build /usr/local/ncbi /usr/local/ncbi</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">COPY --from=build /root/.ncbi /root/.ncbi</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">ENV PATH=/usr/local/ncbi/sra-tools/bin:${PATH}</span></pre>
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<br>
</li>
<li id="b3c4822d491e1dc32917d1df943139c7815d3214">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#b3c4822d491e1dc32917d1df943139c7815d3214"><strong>build/docker/Dockerfile.build-amazonlinux</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">FROM amazonlinux:latest AS build-base</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RUN yum -q -y update && yum -q -y install gcc g++ gcc-c++ make cmake git bison flex uuid-runtime</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">FROM build-base AS build</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">LABEL author="Kenneth Durbrow" \</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> maintainer="kenneth.durbrow@nih.gov" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> vendor="gov.nih.nlm.ncbi" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> website="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software" \</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> repository="https://github.com/ncbi/sra-tools/" \</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> description="Builds and installs the sratoolkit along with a working default configuration"</span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ARG NGS_BRANCH=master</span>
</pre>
</td>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ARG VDB_BRANCH=master</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ARG SRA_BRANCH=master</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">ARG BUILD_STYLE=--without-debug</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">RUN git clone -b ${NGS_BRANCH} --depth 1 https://github.com/ncbi/ngs.git</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">RUN git clone -b ${VDB_BRANCH} --depth 1 https://github.com/ncbi/ncbi-vdb.git</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">RUN git clone -b ${SRA_BRANCH} --depth 1 https://github.com/ncbi/sra-tools.git</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">WORKDIR /ncbi-vdb</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">WORKDIR /ngs</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s -C ngs-sdk >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">WORKDIR /sra-tools</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">RUN make install</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">RUN mkdir -p /root/.ncbi</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">RUN printf '/LIBS/GUID = "%s"\n' `uuidgen` > /root/.ncbi/user-settings.mkfg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">RUN printf '/libs/cloud/report_instance_identity = "true"\n' >> /root/.ncbi/user-settings.mkfg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">RUN printf '/libs/cloud/accept_aws_charges = "true"\n/libs/cloud/accept_gcp_charges = "true"\n' >> /root/.ncbi/user-settings.mkfg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">FROM amazonlinux:latest</span>
</pre>
</td>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">COPY --from=build /etc/ncbi /etc/ncbi</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">COPY --from=build /usr/local/ncbi /usr/local/ncbi</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">COPY --from=build /root/.ncbi /root/.ncbi</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">ENV PATH=/usr/local/ncbi/sra-tools/bin:${PATH}</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">RUN echo "BY USING THIS DOCKER IMAGE IN A CLOUD ENVIRONMENT, YOU WILL BE SENDING YOUR CLOUD INSTANCE IDENTITY TO NCBI, AND YOU AGREE TO ACCEPT ANY CHARGES WHICH MIGHT OCCUR DUE TO TRANSFERING DATA FROM NCBI."</span></pre>
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</li>
<li id="ff7afd81f96a2d28b57295b6979b65b01d0d8b37">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#ff7afd81f96a2d28b57295b6979b65b01d0d8b37"><strong>build/docker/Dockerfile.build-ubuntu</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">FROM ubuntu:bionic AS build-base</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RUN apt-get --quiet update && apt-get --quiet install -y make cmake git gcc g++ flex bison uuid-runtime</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">FORM build-base as build</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">LABEL author="Kenneth Durbrow" \</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> maintainer="kenneth.durbrow@nih.gov" \</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> vendor="gov.nih.nlm.ncbi" \</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> website="https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software" \</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> repository="https://github.com/ncbi/sra-tools/" \</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> description="Builds and installs the sratoolkit along with a working default configuration"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ARG NGS_BRANCH=master</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ARG VDB_BRANCH=master</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ARG SRA_BRANCH=master</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">ARG BUILD_STYLE=--without-debug</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">RUN git clone -b ${NGS_BRANCH} --depth 1 https://github.com/ncbi/ngs.git</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">RUN git clone -b ${VDB_BRANCH} --depth 1 https://github.com/ncbi/ncbi-vdb.git</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">RUN git clone -b ${SRA_BRANCH} --depth 1 https://github.com/ncbi/sra-tools.git</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">WORKDIR /ncbi-vdb</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">WORKDIR /ngs</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s -C ngs-sdk >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">WORKDIR /sra-tools</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">RUN ./configure ${BUILD_STYLE} && make -s >/dev/null 2>&1 || { echo "make failed"; exit 1; }</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">RUN make install</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">RUN mkdir -p /root/.ncbi</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">RUN printf '/LIBS/GUID = "%s"\n' `uuidgen` > /root/.ncbi/user-settings.mkfg</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">RUN printf '/libs/cloud/report_instance_identity = "true"\n' >> /root/.ncbi/user-settings.mkfg</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">RUN printf '/libs/cloud/accept_aws_charges = "true"\n/libs/cloud/accept_gcp_charges = "true"\n' >> /root/.ncbi/user-settings.mkfg</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">FROM ubuntu:latest</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">COPY --from=build /etc/ncbi /etc/ncbi</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">COPY --from=build /usr/local/ncbi /usr/local/ncbi</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">COPY --from=build /root/.ncbi /root/.ncbi</span>
</pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">ENV PATH=/usr/local/ncbi/sra-tools/bin:${PATH}</span>
</pre>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">RUN echo "BY USING THIS DOCKER IMAGE IN A CLOUD ENVIRONMENT, YOU WILL BE SENDING YOUR CLOUD INSTANCE IDENTITY TO NCBI, AND YOU AGREE TO ACCEPT ANY CHARGES WHICH MIGHT OCCUR DUE TO TRANSFERING DATA FROM NCBI."</span></pre>
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</li>
<li id="12a90b5d79abffc4b2b26b545f55da6828b9b22a">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#12a90b5d79abffc4b2b26b545f55da6828b9b22a"><strong>build/docker/Dockerfile.delite</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,8 @@</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"># % mkdir ~/output</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"># % docker run -v ~/output/:/output:rw --rm sratoolkit:delite delite_docker.sh SRR000001 SRR000002</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># % docker run -v ~/output/:/output:rw --rm sratoolkit:delite vdb-dump -R 1 /output/SRR000001/new.kar</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"># % docker run -v ~/output/:/output:rw --rm sratoolkit:delite delite_docker.sh --skiptest SRR000001</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># % docker run -v ~/output/:/output:rw --rm sratoolkit:delite delite_test_docker.sh SRR000001</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"># </span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"># bionic is 18.04 LTS</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -36,8 +38,8 @@ RUN make install</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">FROM build AS delited</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">### Install delite process binaries and script</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">RUN cp -a /root/ncbi-outdir/sra-tools/*/*/*/*/bin/kar+* /root/ncbi-outdir/sra-tools/*/*/*/*/bin/make-read-filter* /sra-tools/tools/kar/sra_delite.sh /sra-tools/tools/kar/sra_delite.kfg /sra-tools/tools/kar/delite_docker.sh /usr/local/ncbi/sra-tools/bin</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">RUN chmod ugo+x /usr/local/ncbi/sra-tools/bin/delite_docker.sh</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">RUN cp -a /root/ncbi-outdir/sra-tools/*/*/*/*/bin/kar+* /root/ncbi-outdir/sra-tools/*/*/*/*/bin/make-read-filter* /sra-tools/tools/kar/sra_delite.sh /sra-tools/tools/kar/sra_delite.kfg /sra-tools/tools/kar/delite_docker.sh /<span class="idiff left right">sra-tools/tools/kar/delite_test_docker.sh /</span>usr/local/ncbi/sra-tools/bin</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">RUN chmod ugo+x /usr/local/ncbi/sra-tools/bin/delite_docker.sh<span class="idiff left right"> /usr/local/ncbi/sra-tools/bin/delite_test_docker.sh</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">### Copy schema files</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">WORKDIR /ncbi-vdb/interfaces</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">RUN rm -rf csra2 sra/pevents.* ; for i in */*.vschema ; do mkdir -p /schema/`dirname $i` ; cp $i /schema/`dirname $i` ; done ; rm -f /schema/ncbi/trace.vschema</span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sra-sdk (2.10.7+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Set field Upstream-Contact in debian/copyright.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Repository-Browse.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove obsolete field Contact from debian/upstream/metadata (already present</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> in machine-readable debian/copyright).</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Tue, 02 Jun 2020 21:47:38 -0400</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">sra-sdk (2.10.6+dfsg-5) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * debian/patches/reenable_legacy_schema_in_sra_load.patch: New patch to</span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,6 +10,7 @@ Files-Excluded: */libs/ext</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> */ld.mac*</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> */ld.win*</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> */win-cc.sh</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Upstream-Contact: sra-tools@ncbi.nlm.nih.gov</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Copyright: none claimed</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,4 +65,3 @@ License: unrestricted</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> The test data files contained in the archive are a data set prepared from</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> original SRAs with accession numbers SRR6650398, SRR2042184 and SRR7032226.</span></pre>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,4 +80,3 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext">override_dh_prep:</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> dh_prep -X debian/tmp</span></pre>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Contact: sra-tools@ncbi.nlm.nih.gov</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/ncbi/sra-tools/issues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/ncbi/sra-tools/issues/new</span>
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2
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Reference:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Author: ></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Rasko Leinonen and Ruth Akhtar and Ewan Birney and James Bonfield and</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,3 +30,5 @@ Registry:</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> Entry: OMICS_03771</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> Entry: sra-tools</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Repository: https://github.com/ncbi/sra-tools.git</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Repository-Browse: https://github.com/ncbi/sra-tools</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#4705a68e02a22c6bfea0273af010dd42e1861b4a"><strong>shared/toolkit.vers</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.10.<span class="idiff left right">6</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.10.<span class="idiff left right">7</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x020A000<span class="idiff left right">6</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOOLKIT_VERS 0x020A000<span class="idiff left right">7</span></span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#b3f7be8d2cddbea73a24a16a7011a3dce42fa650"><strong>test/driver-tool/Makefile</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,7 @@ MODULE = test/driver-tool</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"><span class="k" style="font-weight: 600;">include</span><span class="sx" style="color: #d14;"> $(TOP)/build/Makefile.env</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="make"><span class="nl">runtests</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">built-in bogus container good</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="make"><span class="nl">runtests</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">built-in bogus container good<span class="idiff left right"> vdbcache</span></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nv" style="color: #008080;">TMPDIR</span> <span class="o" style="font-weight: 600;">?=</span> /tmp</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nv" style="color: #008080;">TEMPDIR</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nv" style="color: #008080;">$(TMPDIR)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,5 +96,14 @@ $(CONTAINER): | actual mkfg</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="make"> <span class="nv" style="color: #008080;">$(BINDIR)</span>/sratools <span class="nv" style="color: #008080;">$@</span> 2>actual/<span class="nv" style="color: #008080;">$@</span>.stderr <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="make"> diff expected/<span class="nv" style="color: #008080;">$@</span>.stderr actual/<span class="nv" style="color: #008080;">$@</span>.stderr</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">runtests bogus container good $(CONTAINER) $(GOOD)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="make"><span class="nl">vdbcache</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">| actual mkfg</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="make"> <span class="p">@</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"testing expected output for run with vdbcache"</span> <span class="p">;</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="make"> <span class="nv" style="color: #008080;">NCBI_SETTINGS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(TEMPDIR)</span>/tmp.mkfg <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="make"> <span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$(BINDIR)</span>:<span class="nv" style="color: #008080;">$$</span>PATH <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="make"> <span class="nv" style="color: #008080;">SRATOOLS_TESTING</span><span class="o" style="font-weight: 600;">=</span>5 <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="make"> <span class="nv" style="color: #008080;">SRATOOLS_IMPERSONATE</span><span class="o" style="font-weight: 600;">=</span>vdb-dump <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="make"> <span class="nv" style="color: #008080;">$(BINDIR)</span>/sratools SRR390728 2>actual/<span class="nv" style="color: #008080;">$@</span>.stderr <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="make"> diff expected/<span class="nv" style="color: #008080;">$@</span>.stderr actual/<span class="nv" style="color: #008080;">$@</span>.stderr</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">runtests bogus container good $(CONTAINER) $(GOOD) vdbcache</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="make"><span class="nl">.INTERMEDIATE</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(TEMPDIR)/tmp.mkfg</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#a08ddce7c6ffbea3e906dc17b4fc2835b13a1859"><strong>test/driver-tool/expected/vdbcache.stderr</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">VDB_REMOTE_URL</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">VDB_REMOTE_VDBCACHE</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#14865266faebea48f0221b2afc675b1d701f864b"><strong>tools/driver-tool/imp_fasterq_dump.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,7 @@ struct FasterqParams final : CmnOptAndAccessions</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">cmdline</span> <span class="p">.</span> <span class="n" style="color: #333;">addOption</span> <span class="p">(</span> <span class="n" style="color: #333;">Threads</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ThreadsCount</span><span class="p">,</span> <span class="s" style="color: #d14;">"e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="s" style="color: #d14;">"<count>"</span><span class="p">,</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="s" style="color: #d14;">"how many threads to use (dflt=6)"</span> <span class="p">);</span></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">cmdline</span> <span class="p">.</span> <span class="n" style="color: #333;">addOption</span> <span class="p">(</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="s" style="color: #d14;">"p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"progres"</span><span class="p">,</span> <span class="s" style="color: #d14;">"show progress (not possible if stdout used)"</span> <span class="p">);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">cmdline</span> <span class="p">.</span> <span class="n" style="color: #333;">addOption</span> <span class="p">(</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="s" style="color: #d14;">"p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"progres<span class="idiff left right">s</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"show progress (not possible if stdout used)"</span> <span class="p">);</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">cmdline</span> <span class="p">.</span> <span class="n" style="color: #333;">addOption</span> <span class="p">(</span> <span class="n" style="color: #333;">details</span><span class="p">,</span> <span class="s" style="color: #d14;">"x"</span><span class="p">,</span> <span class="s" style="color: #d14;">"details"</span><span class="p">,</span> <span class="s" style="color: #d14;">"print details of all options selected"</span> <span class="p">);</span></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">cmdline</span> <span class="p">.</span> <span class="n" style="color: #333;">addOption</span> <span class="p">(</span> <span class="n" style="color: #333;">split_spot</span><span class="p">,</span> <span class="s" style="color: #d14;">"s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"split-spot"</span><span class="p">,</span> <span class="s" style="color: #d14;">"split spots into reads"</span> <span class="p">);</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">cmdline</span> <span class="p">.</span> <span class="n" style="color: #333;">addOption</span> <span class="p">(</span> <span class="n" style="color: #333;">split_files</span><span class="p">,</span> <span class="s" style="color: #d14;">"S"</span><span class="p">,</span> <span class="s" style="color: #d14;">"split-files"</span><span class="p">,</span> <span class="s" style="color: #d14;">"write reads into different files"</span> <span class="p">);</span></span>
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<li id="e7acf3882da8bde42f6b4ae537f55850c8352c0e">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#e7acf3882da8bde42f6b4ae537f55850c8352c0e"><strong>tools/driver-tool/proc.posix.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,6 +111,11 @@ static void debugPrintDryRun( char const *const toolpath</td>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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112
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"><span class="p">{</span></span>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">logging_state</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing_level</span><span class="p">())</span> <span class="p">{</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">make_sequence</span><span class="p">(</span><span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="p">(),</span> <span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">END_ENUM</span><span class="p">))</span> <span class="p">{</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">debugPrintEnvVarName</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="p">}</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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114
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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115
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">make_sequence</span><span class="p">(</span><span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="p">(),</span> <span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">END_ENUM</span><span class="p">))</span> <span class="p">{</span></span>
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116
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">debugPrintEnvVar</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<li id="7ecd87d0626d38b13c6f315651f9b239fdd2f04e">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#7ecd87d0626d38b13c6f315651f9b239fdd2f04e"><strong>tools/driver-tool/proc.win32.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,6 +146,11 @@ static bool debugPrintDryRun(char const *const toolpath</td>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">logging_state</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">testing_level</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">make_sequence</span><span class="p">(</span><span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="p">(),</span> <span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">END_ENUM</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">debugPrintEnvVarName</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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149
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">4</span><span class="p">:</span></span>
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150
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">make_sequence</span><span class="p">(</span><span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="p">(),</span> <span class="n" style="color: #333;">constants</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">END_ENUM</span><span class="p">))</span> <span class="p">{</span></span>
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151
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">debugPrintEnvVar</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<li id="4015bd19657723f593dae74db9fa526e45f7755c">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#4015bd19657723f593dae74db9fa526e45f7755c"><strong>tools/driver-tool/run-source.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -375,13 +375,13 @@ Dictionary data_source::get_environment() const</td>
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375
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">REMOTE_NEED_PMT</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span></span>
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376
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="cpp"></span>
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377
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">haveVdbCache</span><span class="p">)</span> <span class="p">{</span></span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">REMOTE_<span class="idiff left right">URL</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">remoteUrl</span><span class="p">;</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">REMOTE_<span class="idiff left right">VDBCACHE</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">remoteUrl</span><span class="p">;</span></span>
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379
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">haveCachePath</span><span class="p">)</span></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CACHE_<span class="idiff left right">URL</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">cachePath</span><span class="p">;</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CACHE_<span class="idiff left right">VDBCACHE</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">cachePath</span><span class="p">;</span></span>
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381
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">haveLocalPath</span><span class="p">)</span></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LOCAL_<span class="idiff left right">URL</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">localPath</span><span class="p">;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">LOCAL_<span class="idiff left right">VDBCACHE</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">localPath</span><span class="p">;</span></span>
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">haveSize</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIZE_<span class="idiff left right">URL</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">fileSize</span><span class="p">;</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SIZE_<span class="idiff left right">VDBCACHE</span></span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">fileSize</span><span class="p">;</span></span>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">needCE</span><span class="p">)</span></span>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">names</span><span class="p">[</span><span class="n" style="color: #333;">env_var</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CACHE_NEED_CE</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span></span>
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">haveVdbCache</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">vdbcache</span><span class="p">.</span><span class="n" style="color: #333;">needPmt</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#c3bfe0034bfa0fac040930a7f68aba030133bf56"><strong>tools/driver-tool/util.hpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,3 +138,10 @@ static inline void debugPrintEnvVar(char const *const name, bool const continuel</td>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"='"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">continueline</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\\\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"><span class="p">}</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">debugPrintEnvVarName</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="k" style="font-weight: 600;">const</span> <span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">continueline</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"><span class="p">{</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">EnvironmentVariables</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">continueline</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" </span><span class="se" style="color: #d14;">\\\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#592b3936f061b2aa3ca7c7be73c3fd377947e5b0"><strong>tools/kar/DL/INSTALL.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#THIS is not a script ... lol</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell">usage <span class="o" style="font-weight: 600;">()</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nv" style="color: #008080;">AGA</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AGA</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> echo</span> <span class="nv" style="color: #008080;">$AGA</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> >&2</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="sh" style="color: #d14;">This script will install or update delite binaries in somewhere</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
</pre>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="sh" style="color: #d14;">Syntax: `basename </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;">` [-n] directory_where_to_install</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="sh" style="color: #d14;">Where:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="sh" style="color: #d14;"> -n - file will be updated only if there is newer version</span></span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nv" style="color: #008080;">NEW_ONLY</span><span class="o" style="font-weight: 600;">=</span>0</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;">case</span> <span class="nv" style="color: #008080;">$# </span><span class="k" style="font-weight: 600;">in</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>1<span class="p">)</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nv" style="color: #008080;">TARGET_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="p">;;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> 2<span class="p">)</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$1</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"-n"</span> <span class="o" style="font-weight: 600;">]</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">NEW_ONLY</span><span class="o" style="font-weight: 600;">=</span>1</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>usage ERROR: invalid argument <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$1</span><span class="se" style="color: #d14;">\'</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TARGET_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="p">;;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> usage ERROR: invalid arguments</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"> <span class="p">;;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TARGET_DIR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: target directory is not defined <span class="o" style="font-weight: 600;">></span>&2</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Looking to place where is everything</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nv" style="color: #008080;">INSDIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$0</span> <span class="si" style="color: #d14;">)</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="nv" style="color: #008080;">VER_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$INSDIR</span>/VER</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VER_DIR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: can not <span class="nb" style="color: #0086b3;">stat </span>version directory <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$VER_DIR</span><span class="se" style="color: #d14;">\'</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Some usefuls</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell">run_cmd <span class="o" style="font-weight: 600;">()</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"> <span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>WARNING: run_cmd called with empty arguments <span class="o" style="font-weight: 600;">></span>&2</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## </span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: <span class="nb" style="color: #0086b3;">command </span>failed <span class="o" style="font-weight: 600;">></span>&2</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Looking for target directory</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell">check_make_dir <span class="o" style="font-weight: 600;">()</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Creating directory '</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">'"</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: failed to create directory <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$1</span><span class="se" style="color: #d14;">\'</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell">check_make_dir <span class="nv" style="color: #008080;">$TARGET_DIR</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Copy binaries</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="nv" style="color: #008080;">BIN_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$VER_DIR</span>/BIN</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="nv" style="color: #008080;">BIN_DST</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/bin</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell">check_make_dir <span class="nv" style="color: #008080;">$BIN_DST</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NEW_ONLY</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"1"</span> <span class="nt" style="color: #000080;">-a</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$BIN_DST</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Updating newer binaries"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$BIN_SRC</span><span class="sb" style="color: #d14;">`</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"> <span class="k" style="font-weight: 600;">do</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">SF</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BIN_SRC</span>/<span class="nv" style="color: #008080;">$i</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"> <span class="nv" style="color: #008080;">DF</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BIN_DST</span>/<span class="nv" style="color: #008080;">$i</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SF</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-nt</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DF</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-pP</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SF</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DF</span><span class="s2" style="color: #d14;">"</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## SKIP: </span><span class="nv" style="color: #008080;">$i</span><span class="s2" style="color: #d14;">"</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"><span class="k" style="font-weight: 600;"> done</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Replacing binaries"</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">$BIN_DST</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-rpP</span> <span class="nv" style="color: #008080;">$BIN_SRC</span> <span class="nv" style="color: #008080;">$BIN_DST</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Copy schemas</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="shell"><span class="nv" style="color: #008080;">SCM_SRC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$VER_DIR</span>/SCM</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell"><span class="nv" style="color: #008080;">SCM_DST</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/schema</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="shell">check_make_dir <span class="nv" style="color: #008080;">$SCM_DST</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NEW_ONLY</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"1"</span> <span class="o" style="font-weight: 600;">]</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Updating newer schemas"</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>SF <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: #008080;">$SCM_SRC</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.vschema"</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="shell"> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">DF</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$SCM_DST</span>/<span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$SF</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s#</span><span class="nv" style="color: #008080;">$SCM_SRC</span><span class="s2" style="color: #d14;">##1"</span> <span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SF</span><span class="s2" style="color: #d14;">"</span> <span class="nt" style="color: #000080;">-nt</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DF</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">FDO</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$DF</span> <span class="si" style="color: #d14;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$FDO</span> <span class="o" style="font-weight: 600;">]</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$FDO</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-pP</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SF</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DF</span><span class="s2" style="color: #d14;">"</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## SKIP: </span><span class="nv" style="color: #008080;">$SF</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="shell"><span class="k" style="font-weight: 600;"> done</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## Replacing schemas"</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="shell"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">$SCM_DST</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-rpP</span> <span class="nv" style="color: #008080;">$SCM_SRC</span> <span class="nv" style="color: #008080;">$SCM_DST</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: #008080;">$SCM_DST</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> trace.vschema<span class="sb" style="color: #d14;">`</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$i</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="shell"></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="shell"><span class="nv" style="color: #008080;">UPDD</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$TARGET_DIR</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="shell"><span class="nv" style="color: #008080;">UPDS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$UPDD</span>/UPDATE.sh</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="shell"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Generating update script : <span class="nv" style="color: #008080;">$UPDS</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="shell"></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> > </span><span class="nv" style="color: #008080;">$UPDS</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="shell"><span class="sh" style="color: #d14;">#!/bin/bash</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="shell"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="shell"><span class="sh" style="color: #d14;">echo Update: </span><span class="nv" style="color: #008080;">$UPDD</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="shell"><span class="nv" style="color: #008080;">$INSDIR</span><span class="sh" style="color: #d14;">/INSTALL.sh </span><span class="nv" style="color: #008080;">$UPDD</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="shell"><span class="sh" style="color: #d14;">if [ </span><span class="nv" style="color: #008080;">$?</span><span class="sh" style="color: #d14;"> -ne 0 ]</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="shell"><span class="sh" style="color: #d14;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="shell"><span class="sh" style="color: #d14;"> echo UPDATE FAILED>&2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="shell"><span class="sh" style="color: #d14;"> exit 1</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="shell"><span class="sh" style="color: #d14;">fi</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="shell"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="shell"><span class="sh" style="color: #d14;">echo ENJOY</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="shell"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod </span>774 <span class="nv" style="color: #008080;">$UPDS</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="shell"></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>For future update binaries, please run script <span class="nv" style="color: #008080;">$UPDS</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="shell"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>DONE</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="shell"></span></pre>
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<li id="eab221163ac330a719d4d2b7ed7243757b2ca228">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#eab221163ac330a719d4d2b7ed7243757b2ca228"><strong>tools/kar/DL/README.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">This directory contains scirpts necessary for DELITE testing.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Scritp UPD.sh will create bundle of binaries and scripts, which may be distributed </span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">with script INSTALL.sh</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Script TEST.sh is umbrella for sra_delite.sh</span></pre>
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<li id="b8cf9ca5f34822ff00bfc50c41eb014d5e8fbc9a">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#b8cf9ca5f34822ff00bfc50c41eb014d5e8fbc9a"><strong>tools/kar/DL/TEST.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#####</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## This test script</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#####</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">DD</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$0</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">BIN_D</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$0</span> <span class="si" style="color: #d14;">)</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nv" style="color: #008080;">BASE_D</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$BIN_D</span> <span class="si" style="color: #d14;">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nv" style="color: #008080;">TEST_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BASE_D</span>/test</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">SCM_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BASE_D</span>/schema</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">run_cmd <span class="o" style="font-weight: 600;">()</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nv" style="color: #008080;">ARA</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ARA</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>WARNING: no arguments passed to run_cmd <span class="o" style="font-weight: 600;">></span>&2</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> echo</span> <span class="s2" style="color: #d14;">"########"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## </span><span class="nv" style="color: #008080;">$ARA</span><span class="s2" style="color: #d14;">"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$ARA</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"> <span class="nv" style="color: #008080;">RETC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$?</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$RETC</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"ERROR: command failed (</span><span class="nv" style="color: #008080;">$RETC</span><span class="s2" style="color: #d14;">)"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: #008080;">$RETC</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SCM_D</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: can not <span class="nb" style="color: #0086b3;">stat </span>schema directory <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$SCM_D</span><span class="se" style="color: #d14;">\'</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TEST_D</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$TEST_D</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-ne</span> 1 <span class="o" style="font-weight: 600;">]</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>Usage : <span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$0</span> <span class="si" style="color: #d14;">)</span> ACCESSION <span class="o" style="font-weight: 600;">></span>&2</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nv" style="color: #008080;">ACCESSION</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nv" style="color: #008080;">DST_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TEST_D</span>/<span class="nv" style="color: #008080;">$ACCESSION</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>DELITE: <span class="nv" style="color: #008080;">$ACCESSION</span> to <span class="nv" style="color: #008080;">$DST_D</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## 1 Exporting</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell">run_cmd <span class="nv" style="color: #008080;">$BIN_D</span>/sra_delite.sh import <span class="nt" style="color: #000080;">--accession</span> <span class="nv" style="color: #008080;">$ACCESSION</span> <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$DST_D</span> <span class="nt" style="color: #000080;">--force</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## 2 Deliting</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell">run_cmd <span class="nv" style="color: #008080;">$BIN_D</span>/sra_delite.sh delite <span class="nt" style="color: #000080;">--schema</span> <span class="nv" style="color: #008080;">$SCM_D</span> <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$DST_D</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## 3 Exporting</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell">run_cmd <span class="nv" style="color: #008080;">$BIN_D</span>/sra_delite.sh <span class="nb" style="color: #0086b3;">export</span> <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$DST_D</span> <span class="nt" style="color: #000080;">--force</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>ENJOY!</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"></span></pre>
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<li id="a16d6626c5540e9be51b5f42f421e52ae8e67244">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#a16d6626c5540e9be51b5f42f421e52ae8e67244"><strong>tools/kar/DL/UPD.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## That script will update binaries and schemas for delite to current directory</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Syntax: UPD.sh [--help|-h]</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Directories with sources :</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## /panfs/pan1/sra-test/vdb3/git/inst</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## ~/work/Kar+/sra-tools/tools/kar</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Structure:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## .../BIN - THAT BINARY is in here</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## .../REP - repository</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## |-- VER - version of data</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## |-- BIN - binaries</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## |-- SCM - schemas</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## .../VER - link to current version</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## .../TMP - temparary directory</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Directories with data sources</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">DBIN_DIR</span><span class="o" style="font-weight: 600;">=</span>/panfs/pan1/sra-test/KinDzaDza/Ku/blue/bin</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Other directories and links</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">BIN_D</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$0</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">)</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nv" style="color: #008080;">BASE_D</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">cd</span> <span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$BIN_D</span><span class="s2" style="color: #d14;">"</span> <span class="si" style="color: #d14;">)</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">pwd</span> <span class="si" style="color: #d14;">)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nv" style="color: #008080;">REP_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BASE_D</span>/REP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nv" style="color: #008080;">VER_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BASE_D</span>/VER</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nv" style="color: #008080;">TMP_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$BASE_D</span>/TMP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$REP_D</span> <span class="nv" style="color: #008080;">$VER_D</span> <span class="nv" style="color: #008080;">$TMP_D</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$i</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>WARNING: directory missed <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$i</span><span class="se" style="color: #d14;">\"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">></span>/dev/null 2>&1</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: can not create directory <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$i</span><span class="se" style="color: #d14;">\"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Arguments and envir</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell">usage <span class="o" style="font-weight: 600;">()</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span> <span class="no" style="color: #008080;">EOF</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="sh" style="color: #d14;">That script will update binares and schemas for delite project. By default, it will </span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="sh" style="color: #d14;">put binaries to the same location where script is, and it will put schemas to directory</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="sh" style="color: #d14;">'schemas', which has the same parent directory as script location.</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="sh" style="color: #d14;">Syntax: `basename </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;">` [--help|-h]</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="sh" style="color: #d14;">Where:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="sh" style="color: #d14;"> --help|-h - will show that message</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$@</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="nv" style="color: #008080;">$i</span> <span class="k" style="font-weight: 600;">in</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> <span class="nt" style="color: #000080;">--help</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"> usage</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> <span class="p">;;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"> <span class="nt" style="color: #000080;">-h</span><span class="p">)</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"> usage</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"> <span class="p">;;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>ERROR: invalid argument <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$i</span><span class="se" style="color: #d14;">\"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"> usage</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"> <span class="p">;;</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Something we should put here</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell">run_cmd <span class="o" style="font-weight: 600;">()</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"> <span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: invalid usage <span class="se" style="color: #d14;">\"</span>run_cmd<span class="se" style="color: #d14;">\"</span><span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## </span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: <span class="nb" style="color: #0086b3;">command </span>failed <span class="o" style="font-weight: 600;">></span>&2</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## removing data from previous builds</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$TMP_D</span><span class="sb" style="color: #d14;">`</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$TMP_D</span>/<span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$i</span> <span class="si" style="color: #d14;">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## First we should make a new version</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="nv" style="color: #008080;">TMP_VER</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_D</span>/VER</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMP_VER</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>WARNING: removing old bundle directory <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$TMP_VER</span><span class="se" style="color: #d14;">\"</span><span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">$TMP_VER</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: can not remove old bundle directory <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$TMP_VER</span><span class="se" style="color: #d14;">\"</span><span class="nb" style="color: #0086b3;">.</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"><span class="nv" style="color: #008080;">TMP_BIN</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_VER</span>/BIN</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"><span class="nv" style="color: #008080;">TMP_SCM</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_VER</span>/SCM</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$TMP_VER</span> <span class="nv" style="color: #008080;">$TMP_BIN</span> <span class="nv" style="color: #008080;">$TMP_SCM</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$i</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="shell"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Copying binaries</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="shell"></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell">copy_f <span class="o" style="font-weight: 600;">()</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$@</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell"> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">FILES</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$SRC_D</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}*</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: can nog <span class="nb" style="color: #0086b3;">stat </span>appropriate files <span class="k" style="font-weight: 600;">for</span> <span class="se" style="color: #d14;">\'</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}*</span><span class="se" style="color: #d14;">\'</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="shell"><span class="k" style="font-weight: 600;"> for </span>u <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">ls</span> <span class="nv" style="color: #008080;">$SRC_D</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">i</span><span class="k" style="font-weight: 600;">}*</span><span class="sb" style="color: #d14;">`</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="shell"> <span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">FOH</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: #008080;">$u</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-pP</span> <span class="nv" style="color: #008080;">$SRC_D</span>/<span class="nv" style="color: #008080;">$FOH</span> <span class="nv" style="color: #008080;">$DST_D</span>/<span class="nv" style="color: #008080;">$FOH</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="shell"><span class="k" style="font-weight: 600;"> done</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="shell"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## Here we are copying binaries</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="shell">copy_bins <span class="o" style="font-weight: 600;">()</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"###################################################"</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"## CP BIN: </span><span class="nv" style="color: #008080;">$TMP_BIN</span><span class="s2" style="color: #d14;">"</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="shell"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="shell"> <span class="nv" style="color: #008080;">BIN2CP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="shell"><span class="s2" style="color: #d14;"> fastq-dump </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="shell"><span class="s2" style="color: #d14;"> kar+ </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="shell"><span class="s2" style="color: #d14;"> kar+meta </span><span class="se" style="color: #d14;">\</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="shell"><span class="s2" style="color: #d14;"> make-read-filter </span><span class="se" style="color: #d14;">\</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="shell"><span class="s2" style="color: #d14;"> prefetch </span><span class="se" style="color: #d14;">\</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="shell"><span class="s2" style="color: #d14;"> srapath </span><span class="se" style="color: #d14;">\</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="shell"><span class="s2" style="color: #d14;"> sratools </span><span class="se" style="color: #d14;">\</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="shell"><span class="s2" style="color: #d14;"> vdb-diff </span><span class="se" style="color: #d14;">\</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="shell"><span class="s2" style="color: #d14;"> vdb-dump </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="shell"><span class="s2" style="color: #d14;"> vdb-lock </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="shell"><span class="s2" style="color: #d14;"> vdb-unlock </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="shell"><span class="s2" style="color: #d14;"> vdb-validate </span><span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="shell"><span class="s2" style="color: #d14;"> vdb-config </span><span class="se" style="color: #d14;">\</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="shell"><span class="s2" style="color: #d14;"> "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="shell"> <span class="nv" style="color: #008080;">SRC_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$DBIN_DIR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="shell"> <span class="nv" style="color: #008080;">DST_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_BIN</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="shell"> copy_f <span class="nv" style="color: #008080;">$BIN2CP</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## copying scripts</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## copyinng schemas</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="shell">copy_schemas <span class="o" style="font-weight: 600;">()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
</pre>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>CP SCM: <span class="nv" style="color: #008080;">$TMP_SCM</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="shell"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="shell"> run_cmd git clone <span class="nt" style="color: #000080;">-b</span> engineering https://github.com/ncbi/ncbi-vdb.git <span class="nv" style="color: #008080;">$TMP_D</span>/ncbi-vdb</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="shell"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="shell"> <span class="nv" style="color: #008080;">DSCM_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_D</span>/ncbi-vdb/interfaces</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="shell"></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="shell"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="shell"> <span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span>find <span class="nv" style="color: #008080;">$DSCM_DIR</span> <span class="nt" style="color: #000080;">-type</span> f <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.vschema"</span><span class="sb" style="color: #d14;">`</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="shell"> <span class="k" style="font-weight: 600;">do</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">FF</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$i</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s#</span><span class="nv" style="color: #008080;">$DSCM_DIR</span><span class="s2" style="color: #d14;">##1"</span> <span class="si" style="color: #d14;">)</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="shell"> <span class="nv" style="color: #008080;">DNM</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">dirname</span> <span class="nv" style="color: #008080;">$FF</span> <span class="si" style="color: #d14;">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="shell"> <span class="nv" style="color: #008080;">DSTD</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_SCM</span>/<span class="nv" style="color: #008080;">$DNM</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DSTD</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: #008080;">$DSTD</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$i</span> <span class="nv" style="color: #008080;">$DSTD</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="shell"> <span class="k" style="font-weight: 600;">done</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="shell"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">FF</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TMP_SCM</span><span class="s2" style="color: #d14;">/ncbi/trace.vschema"</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$FF</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$FF</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="shell">copy_scripts <span class="o" style="font-weight: 600;">()</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## Here we are copying scripts</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>CP SCR: <span class="nv" style="color: #008080;">$TMP_BIN</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="shell"> run_cmd git clone <span class="nt" style="color: #000080;">-b</span> engineering https://github.com/ncbi/sra-tools.git <span class="nv" style="color: #008080;">$TMP_D</span>/sra-tools</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="shell"></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="shell"> <span class="nv" style="color: #008080;">SCR2CP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" </span><span class="se" style="color: #d14;">\</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="shell"><span class="s2" style="color: #d14;"> sra_delite.sh </span><span class="se" style="color: #d14;">\</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="shell"><span class="s2" style="color: #d14;"> sra_delite.kfg </span><span class="se" style="color: #d14;">\</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="shell"><span class="s2" style="color: #d14;"> README.txt </span><span class="se" style="color: #d14;">\</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="shell"><span class="s2" style="color: #d14;"> "</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="shell"> <span class="nv" style="color: #008080;">SRC_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_D</span>/sra-tools/tools/kar</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="shell"> <span class="nv" style="color: #008080;">DST_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_BIN</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="shell"></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="shell"> copy_f <span class="nv" style="color: #008080;">$SCR2CP</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="shell"> <span class="nv" style="color: #008080;">SCR2CP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" </span><span class="se" style="color: #d14;">\</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="shell"><span class="s2" style="color: #d14;"> TEST.sh </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="shell"><span class="s2" style="color: #d14;"> "</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="shell"> <span class="nv" style="color: #008080;">SRC_D</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TMP_D</span>/sra-tools/tools/kar/DL</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="shell"></span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="shell"> copy_f <span class="nv" style="color: #008080;">$SCR2CP</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="shell"></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$TMP_D</span>/sra-tools</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="shell"></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="shell">make_prep <span class="o" style="font-weight: 600;">()</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="shell"> <span class="nv" style="color: #008080;">FUFIL</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">date</span> +%y-%m-%d_%H:%M <span class="si" style="color: #d14;">)</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="shell"></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$FUFIL</span> <span class="o" style="font-weight: 600;">></span><span class="nv" style="color: #008080;">$TMP_VER</span>/version</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$REP_D</span><span class="s2" style="color: #d14;">/</span><span class="nv" style="color: #008080;">$FUFIL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="nv" style="color: #008080;">$REP_D</span>/<span class="nv" style="color: #008080;">$FUFIL</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>run_cmd <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$TMP_VER</span> <span class="nv" style="color: #008080;">$REP_D</span>/<span class="nv" style="color: #008080;">$FUFIL</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-rp</span> <span class="nv" style="color: #008080;">$REP_D</span>/<span class="nv" style="color: #008080;">$FUFIL</span> <span class="nv" style="color: #008080;">$BASE_D</span>/<span class="nv" style="color: #008080;">$FUFIL</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$VER_D</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VER_D</span><span class="k" style="font-weight: 600;">}</span>.obsolete</span>
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<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">mv</span> <span class="nv" style="color: #008080;">$BASE_D</span>/<span class="nv" style="color: #008080;">$FUFIL</span> <span class="nv" style="color: #008080;">$VER_D</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="shell"> run_cmd <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VER_D</span><span class="k" style="font-weight: 600;">}</span>.obsolete</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="shell"></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="shell">copy_bins</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="shell"></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="shell">copy_scripts</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="shell"></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="shell">copy_schemas</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="shell">make_prep</span></pre>
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<li id="cfc53ded06dd9f102fec57db7519643932305fd2">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#cfc53ded06dd9f102fec57db7519643932305fd2"><strong>tools/kar/README.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,6 +9,9 @@ The delite process is three stage process :</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">3) packing modified KAR archive with/without reduced data, testing resulting</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> KAR archive with VDB-DIFF program</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">It is should note here, that user could perform testing of resulting KAR archive</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">separately from stage #3/</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Contents:</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">I. Script requirements, environment and configuring.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,6 +20,7 @@ III. Script configuration file</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">IV. Unpacking original KAR archive</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">V. Editing resulting database</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">V|. Exporting data</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">V|-|. Testing data</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">VII. Status</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">VIII. Physical requirements (important, read it)</span>
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22
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">IX. Error codes</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,6 +93,7 @@ list of possible actions :</td>
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89
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"> import - script will download and/or unpack archive to working directory</span>
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90
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> delite - script will perform DELITE on database content</span>
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91
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> export - script will create 'delited' KAR archive</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> test - script will test 'delited' KAR archive</span>
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92
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> status - script will report some status, or whatever.</span>
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93
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>
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94
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">Options could be different for each action, many of them will be discussed</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -245,7 +250,7 @@ perform following:</td>
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245
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">V|. Exporting data</span>
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246
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">=============================================================================</span>
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247
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext">Action 'export' will export delited data into KAR archive and test result.</span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext">There is syntax <span class="idiff left right">of</span> that command:</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">There is syntax <span class="idiff left right">for</span> that command:</span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext"></span>
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250
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext">sra_delite.sh export [ --config CONFIG ] --target TARGET [--force] [--skiptest]</span>
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251
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,6 +268,18 @@ and consistency of schemas, it could take several minutes. The second test will</td>
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263
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext">be done by 'vdb-dump' utility. That test will perform record-by-record data</span>
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264
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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext">comparation for both original and new KAR archives. It is longest test and can</span>
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265
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext">take more than several minutes. User can skip testing by adding flag '--skiptest'.</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">Even if user skipped test, he cound test resulting data later.</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">V|-|. Testing data</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">=============================================================================</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">Action 'test' will test exported delited KAR archive. There is syntax for that</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">command:</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext"></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">sra_delite.sh test [ --config CONFIG ] --target TARGET</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">User should be ready that it could be lengtly procedure. It was introduced for</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">the case if there will be two different queues for deliting and testing results.</span>
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266
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="plaintext"></span>
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267
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="plaintext"></span>
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268
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="plaintext">V|I. Status</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -479,7 +496,7 @@ Now everything is ready for delite process.</td>
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479
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="plaintext">First step user should download docker file, or copy it. The simplest way to download</span>
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480
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="plaintext">docker file is clone sra-toolkit package from GITHUB:</span>
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481
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="plaintext"></span>
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482
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="plaintext"> git clone https://github.com/ncbi/sra-tools.git</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> git clone <span class="idiff left right">-b engineering </span>https://github.com/ncbi/sra-tools.git</span>
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483
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="plaintext"></span>
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484
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext">User could copy docker file to his working directory, and delete sra-toolkit package after.</span>
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485
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -510,6 +527,12 @@ to script and they will be delited sequentially:</td>
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510
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="plaintext"></span>
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511
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="plaintext">In the case of error, script will return error code of failed sra_delite.sh command.</span>
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512
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="plaintext"></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext">If user want to separate delite process and testing results, he can use "delite_docker.sh" command</span>
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<td class="diff-line-num new new_line" data-linenumber="531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext">with "--skiptest" flag, and perform testing after with "delite_test_docker.sh" command:</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext"> docker run -v ~/output/:/output:rw --rm sratoolkit:delite delite_docker.sh --skiptest SRR000001 SRR000002</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"> docker run -v ~/output/:/output:rw --rm sratoolkit:delite delite_test_docker.sh SRR000001 SRR000002</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext"></span>
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513
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="plaintext">NOTE: if there are results of previous delite process for accession, script will exit with</span>
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514
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="plaintext"> error message. User is responsible for deleting these before calling script.</span>
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515
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="plaintext"></span>
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<li id="43b8443c4dd0552a8ddf4c61776ecfa96022cd95">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#43b8443c4dd0552a8ddf4c61776ecfa96022cd95"><strong>tools/kar/delite_docker.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,8 @@</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## run only from docker container. It is umbrella for sra_delite.sh script</span></span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">SKIPTEST_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--skiptest"</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell">usage <span class="o" style="font-weight: 600;">()</span></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> >&2</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +15,7 @@ That script will run delite process on SRA fun by it's accession</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;">Syntax:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"></span>
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<td class="diff-line-num old old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;"> `basename </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;">` < -h | --help | ACCESSION [ACCESSION ...] ></span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="sh" style="color: #d14;"> `basename </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;">` < -h | --help | <span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">$SKIPTEST_TAG</span></span><span class="sh" style="color: #d14;"><span class="idiff right">] </span>ACCESSION [ACCESSION ...] ></span></span>
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17
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
</pre>
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18
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="sh" style="color: #d14;">Where:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,6 +48,16 @@ then</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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48
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">unset </span>SKIPTEST</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$@</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SKIPTEST_TAG</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">SKIPTEST</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$i</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">break</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"></span>
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49
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell">run_cmd <span class="o" style="font-weight: 600;">()</span></span>
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50
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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51
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell"> <span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,6 +79,23 @@ run_cmd ()</td>
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67
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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68
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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69
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell">delite_work_dir <span class="o" style="font-weight: 600;">()</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"> <span class="nv" style="color: #008080;">D2R</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$D2R</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## We do not care about if that command will fail</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>Removing directory <span class="nv" style="color: #008080;">$D2R</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"> vdb-unlock <span class="nv" style="color: #008080;">$D2R</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">$D2R</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>WARNING: can not remove directory <span class="nv" style="color: #008080;">$D2R</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"></span>
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70
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="shell">delite_run <span class="o" style="font-weight: 600;">()</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="shell"> <span class="nv" style="color: #008080;">ACC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,23 +122,13 @@ EOF</td>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="shell"></span>
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94
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="shell"> run_cmd sra_delite.sh delite <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$OUTD</span> <span class="nt" style="color: #000080;">--schema</span> /etc/ncbi/schema</span>
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95
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="shell"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="shell"> run_cmd sra_delite.sh <span class="nb" style="color: #0086b3;">export</span> <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$OUTD</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> run_cmd sra_delite.sh <span class="nb" style="color: #0086b3;">export</span> <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$OUTD</span><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$SKIPTEST</span></span></span>
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97
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="shell"></span>
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98
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## Removing <span class="idiff left right">orig</span> directory</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## Removing <span class="idiff left right">work</span> directory</span></span>
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="shell"></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="shell"> <span class="nv" style="color: #008080;">D2R</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OUTD</span>/orig</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="nv" style="color: #008080;">$D2R</span> <span class="o" style="font-weight: 600;">]</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## We do not care about if that command will fail</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>Removing directory <span class="nv" style="color: #008080;">$D2R</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="shell"> vdb-unlock <span class="nv" style="color: #008080;">$D2R</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> <span class="nv" style="color: #008080;">$D2R</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>WARNING: can not remove directory <span class="nv" style="color: #008080;">$D2R</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"> delite_work_dir <span class="nv" style="color: #008080;">$OUTD</span>/work</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"> delite_work_dir <span class="nv" style="color: #008080;">$OUTD</span>/work.vch</span>
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113
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="shell"></span>
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114
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span></span>
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115
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="shell"><span class="sh" style="color: #d14;">## Finished delite process for </span><span class="nv" style="color: #008080;">$ACC</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,6 +140,11 @@ EOF</td>
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121
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="shell"></span>
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122
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$@</span></span>
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123
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SKIPTEST_TAG</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="shell"><span class="k" style="font-weight: 600;"> continue</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="shell"></span>
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124
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>delite_run <span class="nv" style="color: #008080;">$i</span></span>
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125
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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126
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="shell"></span>
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<li id="5003eb4553c4d457e872976bc5dfa5c1f4f8b93c">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#5003eb4553c4d457e872976bc5dfa5c1f4f8b93c"><strong>tools/kar/delite_test_docker.sh</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## NOTE: That script does not have permissions for execution, because it should</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## run only from docker container. It is umbrella for sra_delite.sh script</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">usage <span class="o" style="font-weight: 600;">()</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> >&2</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="sh" style="color: #d14;">That script will run test results of delite process on SRA run by it's accession</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="sh" style="color: #d14;">Syntax:</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="sh" style="color: #d14;"> `basename </span><span class="nv" style="color: #008080;">$0</span><span class="sh" style="color: #d14;">` < -h | --help | ACCESSION [ACCESSION ...] ></span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="sh" style="color: #d14;">Where:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="sh" style="color: #d14;"> ACCESSION - valid SRA accession</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="sh" style="color: #d14;"> -h | --help - print that help message</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>usage</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo </span>ERROR: ACCESSION parameter is not defined <span class="o" style="font-weight: 600;">></span>&2</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-eq</span> 1 <span class="o" style="font-weight: 600;">]</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;"> case</span> <span class="nv" style="color: #008080;">$1</span> <span class="k" style="font-weight: 600;">in</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="nt" style="color: #000080;">-h</span><span class="p">)</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> usage</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="p">;;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nt" style="color: #000080;">--help</span><span class="p">)</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> usage</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>0</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="p">;;</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"> <span class="k" style="font-weight: 600;">esac</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell">run_cmd <span class="o" style="font-weight: 600;">()</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nv" style="color: #008080;">CMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">"</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: invalid usage or run_cmd <span class="nb" style="color: #0086b3;">command</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> echo</span> <span class="s2" style="color: #d14;">"## </span><span class="nv" style="color: #008080;">$CMD</span><span class="s2" style="color: #d14;">"</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$CMD</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nv" style="color: #008080;">RV</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$?</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$RV</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: <span class="nb" style="color: #0086b3;">command </span>failed with <span class="nb" style="color: #0086b3;">exit </span>code <span class="nv" style="color: #008080;">$RV</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span> <span class="nv" style="color: #008080;">$RV</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell">delite_test <span class="o" style="font-weight: 600;">()</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"> <span class="nv" style="color: #008080;">ACC</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ACC</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo </span>ERROR: invalid usage or delite_test <span class="nb" style="color: #0086b3;">command</span>, ACCESSION missed <span class="o" style="font-weight: 600;">></span>&2</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> </span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="sh" style="color: #d14;">#######################################################################################</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="sh" style="color: #d14;">## Running test on results of delite process for </span><span class="nv" style="color: #008080;">$ACC</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"><span class="sh" style="color: #d14;">## `date`</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> <span class="nv" style="color: #008080;">OUTD</span><span class="o" style="font-weight: 600;">=</span>/output/<span class="nv" style="color: #008080;">$ACC</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"> run_cmd sra_delite.sh <span class="nb" style="color: #0086b3;">test</span> <span class="nt" style="color: #000080;">--target</span> <span class="nv" style="color: #008080;">$OUTD</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"><span class="sh" style="color: #d14;">## Finished test on results of delite process for </span><span class="nv" style="color: #008080;">$ACC</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"><span class="sh" style="color: #d14;">## `date`</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"><span class="sh" style="color: #d14;">#######################################################################################</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>i <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$@</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>delite_test <span class="nv" style="color: #008080;">$i</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"DONE (</span><span class="nv" style="color: #008080;">$@</span><span class="s2" style="color: #d14;">)"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#ec0ea9672f7d4560465210a94264389f1bff4f57"><strong>tools/kar/sra_delite.kfg</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,5 +105,4 @@ diff-exclude MATE_EDIT_DISTANCE</td>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext">### Please, do not allow spaces between parameters</span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"># DELITE_BIN_DIR=/panfs/pan1/trace_work/iskhakov/Tundra/KAR+TST/bin</span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"># USE_OWN_TEMPDIR=1</span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">DELITE_REJECT_VDBCACHE=1</span>
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109
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/b36b20cb22242853e29881740e1cdfc0893143cd...f80fa3d29c2187f911563e3ed3be939a53d58d60#a84cd173c686120c42e6d4c9296132e65c8cb7db"><strong>tools/kar/sra_delite.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,6 +23,7 @@ ORIGINAL_CMD="$0 $@"</td>
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23
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">IMPORT_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"import"</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nv" style="color: #008080;">DELITE_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"delite"</span></span>
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25
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">EXPORT_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"export"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nv" style="color: #008080;">TEST_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"test"</span></span>
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26
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="nv" style="color: #008080;">STATUS_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"status"</span></span>
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27
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"></span>
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28
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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="nv" style="color: #008080;">ACCESSION_TAG</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--accession"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -71,6 +72,7 @@ Where :</td>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="sh" style="color: #d14;"> working directory</span></span>
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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
72
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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$DELITE_TAG</span><span class="sh" style="color: #d14;"> - script will perform DELITE on database content</span></span>
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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
73
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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$EXPORT_TAG</span><span class="sh" style="color: #d14;"> - script will create 'delited' KAR archive</span></span>
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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$TEST_TAG</span><span class="sh" style="color: #d14;"> - script will test 'exported' KAR archive</span></span>
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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
74
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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="sh" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$STATUS_TAG</span><span class="sh" style="color: #d14;"> - script will report some status, or whatever.</span></span>
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75
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"></span>
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76
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="sh" style="color: #d14;">Options:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -112,6 +114,8 @@ case $ACTION in</td>
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112
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="shell"> <span class="p">;;</span></span>
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113
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"> <span class="nv" style="color: #008080;">$EXPORT_TAG</span><span class="p">)</span></span>
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114
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"> <span class="nv" style="color: #008080;">$TEST_TAG</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="shell"> <span class="nv" style="color: #008080;">$STATUS_TAG</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"> <span class="p">;;</span></span>
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117
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="shell"> <span class="k" style="font-weight: 600;">*</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -316,8 +320,6 @@ diff-exclude RIGHT_SOFT_CLIP</td>
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316
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="shell"><span class="sh" style="color: #d14;"># USE_OWN_TEMPDIR=1</span></span>
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<td class="diff-line-num old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="shell"><span class="sh" style="color: #d14;">### That is for docker, and please do not modify it by yourself</span></span>
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318
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="shell"><span class="sh" style="color: #d14;"># DELITE_GUID=</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="shell"><span class="sh" style="color: #d14;">### That is for new version of make-read-filter</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="shell"><span class="sh" style="color: #d14;">DELITE_REJECT_VDBCACHE=1</span></span>
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321
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="shell"></span>
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322
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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323
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -566,9 +568,12 @@ set_resolve_set_dir_values ()</td>
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566
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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567
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="shell"></span>
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568
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TARGET_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TDVAL</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="shell"> <span class="nv" style="color: #008080;">DATABASE_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/orig</span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="shell"> <span class="nv" style="color: #008080;">NEW_KAR_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/new.kar</span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="shell"> <span class="nv" style="color: #008080;">ORIG_KAR_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/orig.kar</span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="shell"> <span class="nv" style="color: #008080;">DATABASE_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/work</span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="shell"> <span class="nv" style="color: #008080;">DATABASE_CACHE_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/work.vch</span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="shell"> <span class="nv" style="color: #008080;">NEW_KAR_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/out</span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="shell"> <span class="nv" style="color: #008080;">NEW_CACHE_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/out.vch</span>
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="shell"> <span class="nv" style="color: #008080;">ORIG_KAR_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/in</span>
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="shell"> <span class="nv" style="color: #008080;">ORIG_CACHE_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/in.vch</span>
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572
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="shell"> <span class="nv" style="color: #008080;">STATUS_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/.status.txt</span>
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573
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="shell"> <span class="nv" style="color: #008080;">VDBCFG_NAME</span><span class="o" style="font-weight: 600;">=</span>vdbconfig.kfg</span>
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="shell"> <span class="nv" style="color: #008080;">VDBCFG_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/<span class="nv" style="color: #008080;">$VDBCFG_NAME</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -581,6 +586,15 @@ set_resolve_set_dir_values</td>
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581
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">NCBI_SETTINGS</span><span class="o" style="font-weight: 600;">=</span>/</span>
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">VDB_CONFIG</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$VDBCFG_NAME</span></span>
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588
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="shell"></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DELITE_GUID</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">UUIDGEN</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> which uuidgen <span class="si" style="color: #d14;">)</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-eq</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">DELITE_GUID</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> uuidgen <span class="si" style="color: #d14;">)</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="shell"></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###############################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## There will be description of status file, which is quite secret file</span></span>
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586
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## ...</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -717,13 +731,13 @@ import_proc ()</td>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="shell"><span class="sh" style="color: #d14;">/sra/quality_type = "raw_scores"</span></span>
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718
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732
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<pre style="margin: 0;"> <span id="LC732" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###</span></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## In the case of AWS, we needed GUID for correct work</span></span>
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722
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<pre style="margin: 0;">-<span id="LC722" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DELITE_GUID</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="shell"><span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> /LIBS/GUID <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$DELITE_GUID</span><span class="se" style="color: #d14;">\"</span> <span class="o" style="font-weight: 600;">>></span><span class="nv" style="color: #008080;">$VDBCFG_FILE</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="shell"><span class="idiff left right"> </span><span class="c" style="color: #998; font-style: italic;">###</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="shell"><span class="idiff left right"> </span><span class="c" style="color: #998; font-style: italic;">## In the case of AWS, we needed GUID for correct work</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="shell"><span class="idiff left right"> </span><span class="c" style="color: #998; font-style: italic;">#</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="shell"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DELITE_GUID</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="shell"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">then</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left right"> </span></span><span class="nb" style="color: #0086b3;">echo</span> /LIBS/GUID <span class="o" style="font-weight: 600;">=</span> <span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$DELITE_GUID</span><span class="se" style="color: #d14;">\"</span> <span class="o" style="font-weight: 600;">>></span><span class="nv" style="color: #008080;">$VDBCFG_FILE</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="shell"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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727
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741
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="shell"></span>
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg Changing directory to <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$TARGET_DIR</span><span class="se" style="color: #d14;">\'</span></span>
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$TARGET_DIR</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -742,24 +756,6 @@ fi</td>
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$TOUTF</span><span class="se" style="color: #d14;">\'</span></span>
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="shell"></span>
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745
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<pre style="margin: 0;">-<span id="LC745" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DELITE_REJECT_VDBCACHE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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746
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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747
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<pre style="margin: 0;">-<span id="LC747" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">VCH</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">ls</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TOUTD</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">*</span>.vdbcache 2>/dev/null <span class="si" style="color: #d14;">)</span></span>
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748
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<pre style="margin: 0;">-<span id="LC748" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VCH</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC750" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOF</span><span class="sh" style="color: #d14;"> >&2</span></span>
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<pre style="margin: 0;">-<span id="LC751" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC752" class="line" lang="shell"><span class="sh" style="color: #d14;">WARNING: This run will not be processed because current make-read-filter</span></span>
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<pre style="margin: 0;">-<span id="LC753" class="line" lang="shell"><span class="sh" style="color: #d14;">utility does not support vdbcache files. Please, try to DELITE that run</span></span>
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754
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<pre style="margin: 0;">-<span id="LC754" class="line" lang="shell"><span class="sh" style="color: #d14;">later, when new version of make-read-filter utility will be available.</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="shell"><span class="sh" style="color: #d14;">Thank You for understanding.</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="shell"><span class="no" style="color: #008080;">EOF</span></span>
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<pre style="margin: 0;">-<span id="LC758" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="shell"> dpec__ 80<span class="p">;</span> err_exit can not process VDBCACHE file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$TOUTF</span><span class="se" style="color: #d14;">\'</span></span>
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760
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<pre style="margin: 0;">-<span id="LC760" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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762
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg Read <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">stat</span> <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"%s"</span> <span class="nv" style="color: #008080;">$TOUTF</span><span class="sb" style="color: #d14;">`</span> bytes to <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$TARGET_DIR</span>/<span class="nv" style="color: #008080;">$TOUTF</span><span class="se" style="color: #d14;">\'</span></span>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="shell"> dpec__ 61<span class="p">;</span> exec_cmd_exit <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$TOUTF</span> <span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -772,6 +768,14 @@ EOF</td>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="shell"></span>
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773
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 62<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$ICMD</span> <span class="nt" style="color: #000080;">--extract</span> <span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span> <span class="nt" style="color: #000080;">--directory</span> <span class="nv" style="color: #008080;">$DATABASE_DIR</span></span>
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774
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="shell"> <span class="nv" style="color: #008080;">TOUTC</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TOUTF</span><span class="k" style="font-weight: 600;">}</span>.vdbcache</span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TOUTC</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg <span class="s2" style="color: #d14;">"Found .VDBCACHE file"</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="shell"> dpec__ 61<span class="p">;</span> exec_cmd_exit <span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$TOUTC</span> <span class="nv" style="color: #008080;">$ORIG_CACHE_FILE</span></span>
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="shell"> dpec__ 62<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$ICMD</span> <span class="nt" style="color: #000080;">--extract</span> <span class="nv" style="color: #008080;">$ORIG_CACHE_FILE</span> <span class="nt" style="color: #000080;">--directory</span> <span class="nv" style="color: #008080;">$DATABASE_CACHE_DIR</span></span>
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## Checking if it is colorspace run</span></span>
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="shell"> check_rejected_run_exit</span>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="shell"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -797,11 +801,25 @@ check_ready_for_delite ()</td>
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>directory <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$SCHEMA_VAL</span><span class="se" style="color: #d14;">\'</span></span>
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="shell"></span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">SCHEMA_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$SCHEMA_VAL</span><span class="p">;</span> <span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SCHEMA_DIR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not resolve directory <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$SCHEMA_VAL</span><span class="se" style="color: #d14;">\'</span></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DATABASE_DIR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>database <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$DATABASE_DIR</span><span class="se" style="color: #d14;">\'</span></span>
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ORIG_CACHE_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DATABASE_CACHE_DIR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>database VDBCACHE <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$DATABASE_CACHE_DIR</span><span class="se" style="color: #d14;">\'</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="shell"></span>
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805
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$STATUS_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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806
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824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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807
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>status file</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -993,7 +1011,7 @@ modify_object ()</td>
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993
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NEW_SCHEMA</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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994
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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995
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg subst <span class="nv" style="color: #008080;">$OLD_SCHEMA</span> to <span class="nv" style="color: #008080;">$NEW_SCHEMA</span></span>
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996
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="shell"> dpec__ 63<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$KARMETA_BIN</span> <span class="nt" style="color: #000080;">--spath</span> <span class="nv" style="color: #008080;">$SCHEMA_<span class="idiff left right">VAL</span></span> <span class="nt" style="color: #000080;">--updschema</span> <span class="nv" style="color: #008080;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$NEW_SCHEMA</span><span class="se" style="color: #d14;">\'</span> <span class="nv" style="color: #008080;">$M2D</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="shell"> dpec__ 63<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$KARMETA_BIN</span> <span class="nt" style="color: #000080;">--spath</span> <span class="nv" style="color: #008080;">$SCHEMA_<span class="idiff left right">DIR</span></span> <span class="nt" style="color: #000080;">--updschema</span> <span class="nv" style="color: #008080;">schema</span><span class="o" style="font-weight: 600;">=</span><span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$NEW_SCHEMA</span><span class="se" style="color: #d14;">\'</span> <span class="nv" style="color: #008080;">$M2D</span></span>
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997
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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998
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>warn_msg no subst found <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: #008080;">$OLD_SCHEMA</span></span>
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999
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1017
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1225,22 +1243,14 @@ check_read_and_quality_len ()</td>
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1225
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1243
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="shell"></span>
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1226
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="shell">test_kar <span class="o" style="font-weight: 600;">()</span></span>
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1227
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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1228
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<pre style="margin: 0;">-<span id="LC1228" class="line" lang="shell"> <span class="nv" style="color: #008080;">F2T</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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1229
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<pre style="margin: 0;">-<span id="LC1229" class="line" lang="shell"></span>
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1230
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<pre style="margin: 0;">-<span id="LC1230" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SKIPTEST_VAL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1232
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<td class="diff-line-num new_line old" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1232" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>warn_msg skipping tests <span class="k" style="font-weight: 600;">for</span> <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$F2T</span><span class="se" style="color: #d14;">\'</span> ...</span>
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1233
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<td class="diff-line-num new_line old" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1233" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span></span>
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1234
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<pre style="margin: 0;">-<span id="LC1234" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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1235
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<td class="diff-line-num new_line old" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1235" class="line" lang="shell"></span>
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1236
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<pre style="margin: 0;">-<span id="LC1236" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>check_read_and_quality_len <span class="nv" style="color: #008080;">$F2T</span></span>
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1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="shell"> check_read_and_quality_len <span class="nv" style="color: #008080;">$NEW_KAR_FILE</span></span>
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1237
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1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="shell"></span>
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1238
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<td class="diff-line-num new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span> <span class="o" style="font-weight: 600;">]</span></span>
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1239
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1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1240
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<td class="diff-line-num new_line old" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1240" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit SKIPPING DIFF TESTS <span class="k" style="font-weight: 600;">for</span> <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$<span class="idiff left right">F2T</span></span><span class="se" style="color: #d14;">\'</span>, can not <span class="nb" style="color: #0086b3;">stat </span>original KAR file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit SKIPPING DIFF TESTS <span class="k" style="font-weight: 600;">for</span> <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$<span class="idiff left right">NEW_KAR_FILE</span></span><span class="se" style="color: #d14;">\'</span>, can not <span class="nb" style="color: #0086b3;">stat </span>original KAR file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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1241
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1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1242
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1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="shell"></span>
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1243
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<pre style="margin: 0;">-<span id="LC1243" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>exec_cmd <span class="nv" style="color: #008080;">$VDBVALIDATE_BIN</span> <span class="nt" style="color: #000080;">-x</span> <span class="nv" style="color: #008080;">$<span class="idiff left right">F2T</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1253
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<pre style="margin: 0;">+<span id="LC1253" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>exec_cmd <span class="nv" style="color: #008080;">$VDBVALIDATE_BIN</span> <span class="nt" style="color: #000080;">-x</span> <span class="nv" style="color: #008080;">$<span class="idiff left right">NEW_KAR_FILE</span></span></span>
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1244
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1254
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span></span>
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1245
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1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1246
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1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>warn_msg vdb-validate step failed, checking original KAR file</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1253,7 +1263,7 @@ test_kar ()</td>
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1253
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1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1254
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1264
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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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1255
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1265
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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="shell"></span>
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1256
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<td class="diff-line-num new_line old" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1256" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TCMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VDBDIFF_BIN</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$<span class="idiff left right">F2T</span></span><span class="s2" style="color: #d14;"> -i"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TCMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VDBDIFF_BIN</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$<span class="idiff left">NEW_KAR_FILE</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> -c</span> -i"</span></span>
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1257
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<td class="diff-line-num new_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1258
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<td class="diff-line-num new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="shell"> <span class="nv" style="color: #008080;">TDC</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DIFFEXCLUDE</span><span class="s2" style="color: #d14;">"</span></span>
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1259
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1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="shell"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1288,18 +1298,32 @@ test_kar ()</td>
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1288
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1298
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<pre style="margin: 0;"> <span id="LC1298" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 68<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$TCMD</span></span>
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<td class="diff-line-num old_line" data-linenumber="1289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1289
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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1290
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1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="shell"></span>
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1291
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<td class="diff-line-num new_line old" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1291" class="line" lang="shell"><span class="idiff left right">kar_new</span> <span class="o" style="font-weight: 600;">()</span></span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="shell"><span class="idiff left right">check_force_remove_old_kar</span> <span class="o" style="font-weight: 600;">()</span></span>
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1292
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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1293
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<pre style="margin: 0;">-<span id="LC1293" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NEW_KAR_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="shell"> <span class="nv" style="color: #008080;">F2R</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="shell"> <span class="nv" style="color: #008080;">MSS</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span></span>
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1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MSS</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">MSS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"KAR"</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$F2R</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1294
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old_line" data-linenumber="1295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1295
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<td class="diff-line-num new_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$FORCE_VAL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1296
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<td class="diff-line-num new_line" data-linenumber="1314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1297
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<td class="diff-line-num new_line old" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg forcing to remove o<span class="idiff left">dl KAR file </span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$NEW_KAR_FILE</span></span><span class="se" style="color: #d14;">\'</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1298
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<td class="diff-line-num new_line old" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="shell"> dpec__ 107<span class="p">;</span> exec_cmd_exit <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;"><span class="idiff left right">$NEW_KAR_FILE</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg forcing to remove o<span class="idiff left">ld </span><span class="nv" style="color: #008080;"><span class="idiff">$MSS</span></span><span class="idiff"> file </span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$F2R</span></span><span class="se" style="color: #d14;">\'</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1316
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<pre style="margin: 0;">+<span id="LC1316" class="line" lang="shell"> dpec__ 107<span class="p">;</span> exec_cmd_exit <span class="nb" style="color: #0086b3;">rm</span> <span class="s2" style="color: #d14;"><span class="idiff left">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$F2R</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="1299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1299
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<td class="diff-line-num new_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1300
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<td class="diff-line-num new_line old" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 106<span class="p">;</span> err_exit old <span class="idiff left">KAR file found </span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$NEW_KAR_FILE</span></span><span class="se" style="color: #d14;">\'</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 106<span class="p">;</span> err_exit old <span class="nv" style="color: #008080;"><span class="idiff left">$MSS</span></span><span class="idiff"> file found </span><span class="se" style="color: #d14;"><span class="idiff">\'</span></span><span class="nv" style="color: #008080;"><span class="idiff right">$F2R</span></span><span class="se" style="color: #d14;">\'</span></span>
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1301
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<td class="diff-line-num new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="1302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1302
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<td class="diff-line-num new_line" data-linenumber="1320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1320
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="shell">kar_new <span class="o" style="font-weight: 600;">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1324
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<pre style="margin: 0;">+<span id="LC1324" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="shell"> check_force_remove_old_kar <span class="nv" style="color: #008080;">$NEW_KAR_FILE</span> KAR</span>
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<td class="diff-line-num new old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="shell"> check_force_remove_old_kar <span class="nv" style="color: #008080;">$NEW_CACHE_FILE</span> .VDBCACHE</span>
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<td class="diff-line-num old_line" data-linenumber="1303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1303
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<td class="diff-line-num new_line" data-linenumber="1327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1304
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<td class="diff-line-num new_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1328
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="shell"> <span class="nv" style="color: #008080;">TCMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$KAR_BIN</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1305
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<td class="diff-line-num new_line" data-linenumber="1329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1329
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<pre style="margin: 0;"> <span id="LC1329" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$FORCE_VAL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1319,7 +1343,20 @@ kar_new ()</td>
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1319
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="shell"></span>
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1320
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1344
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<pre style="margin: 0;"> <span id="LC1344" class="line" lang="shell"> dpec__ 62<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$TCMD</span></span>
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1321
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="shell"></span>
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1322
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<pre style="margin: 0;">-<span id="LC1322" class="line" lang="shell"> test_kar <span class="nv" style="color: #008080;">$NEW_KAR_FILE</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1346
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<pre style="margin: 0;">+<span id="LC1346" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DATABASE_CACHE_DIR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1347
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<pre style="margin: 0;">+<span id="LC1347" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1348
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<pre style="margin: 0;">+<span id="LC1348" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>info_msg <span class="s2" style="color: #d14;">"Creating .VDBCACHE file"</span></span>
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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="shell"></span>
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1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="shell"> <span class="nv" style="color: #008080;">TCMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$KAR_BIN</span><span class="s2" style="color: #d14;">"</span></span>
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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$FORCE_VAL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TCMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TCMD</span><span class="s2" style="color: #d14;"> -f"</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TCMD</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TCMD</span><span class="s2" style="color: #d14;"> --create </span><span class="nv" style="color: #008080;">$NEW_CACHE_FILE</span><span class="s2" style="color: #d14;"> --directory </span><span class="nv" style="color: #008080;">$DATABASE_CACHE_DIR</span><span class="s2" style="color: #d14;">"</span></span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="shell"></span>
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1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="shell"> dpec__ 62<span class="p">;</span> exec_cmd_exit <span class="nv" style="color: #008080;">$TCMD</span></span>
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1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1323
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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1324
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1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="shell"></span>
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1325
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="shell">print_stats <span class="o" style="font-weight: 600;">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1364,12 +1401,86 @@ export_proc ()</td>
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1364
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1401
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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## writing delited kar archive</span></span>
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1365
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1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="shell"> kar_new</span>
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1366
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<td class="diff-line-num new_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1403
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="shell"></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$SKIPTEST_VAL</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>warn_msg skipping tests <span class="k" style="font-weight: 600;">for</span> <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$NEW_KAR_FILE</span><span class="se" style="color: #d14;">\'</span> ...</span>
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<td class="diff-line-num new old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="shell"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>test_kar</span>
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<td class="diff-line-num new old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1367
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<td class="diff-line-num new_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## just printing stats</span></span>
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<td class="diff-line-num old_line" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1368
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<td class="diff-line-num new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1414" class="line" lang="shell"> print_stats</span>
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<td class="diff-line-num old_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1369
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<td class="diff-line-num new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1415
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1415" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1370
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<td class="diff-line-num new_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1416
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1416" class="line" lang="shell"> info_msg <span class="s2" style="color: #d14;">"DONE"</span></span>
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<td class="diff-line-num old_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1371
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<td class="diff-line-num new_line" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1372
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<td class="diff-line-num new_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1418
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1418" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###############################################################################################</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1420
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<pre style="margin: 0;">+<span id="LC1420" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###############################################################################################</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1421
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<pre style="margin: 0;">+<span id="LC1421" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###<<>>### Test</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">##############################################################################################</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1423
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<pre style="margin: 0;">+<span id="LC1423" class="line" lang="shell">check_ready_for_test <span class="o" style="font-weight: 600;">()</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1425
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<pre style="margin: 0;">+<span id="LC1425" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$STATUS_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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1426
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<pre style="margin: 0;">+<span id="LC1426" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1427
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<pre style="margin: 0;">+<span id="LC1427" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>status file</span>
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1428
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<pre style="margin: 0;">+<span id="LC1428" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1429
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<pre style="margin: 0;">+<span id="LC1429" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1430
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<pre style="margin: 0;">+<span id="LC1430" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TVAR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$DELITED_TAG</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">$STATUS_FILE</span> 2>/dev/null<span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1431
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<pre style="margin: 0;">+<span id="LC1431" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TVAR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 86<span class="p">;</span> err_exit status shows that object was not delited yet</span>
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1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>original KAR file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$ORIG_KAR_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NEW_KAR_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1442
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<pre style="margin: 0;">+<span id="LC1442" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>delited KAR file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$NEW_KAR_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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1444
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<pre style="margin: 0;">+<span id="LC1444" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">TVAR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nv" style="color: #008080;">$KARMETA_BIN</span> <span class="nt" style="color: #000080;">--info</span> SOFTWARE/delite <span class="nv" style="color: #008080;">$NEW_KAR_FILE</span> 2>/dev/null<span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1447
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<pre style="margin: 0;">+<span id="LC1447" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TVAR</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1448
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<pre style="margin: 0;">+<span id="LC1448" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 86<span class="p">;</span> err_exit object was not delited yet</span>
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1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1451
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="shell"></span>
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1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-h</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ORIG_CACHE_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1453
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<pre style="margin: 0;">+<span id="LC1453" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$ORIG_CACHE_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1455
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<pre style="margin: 0;">+<span id="LC1455" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1456
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<pre style="margin: 0;">+<span id="LC1456" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat</span> .VDBCACHE <span class="k" style="font-weight: 600;">for </span>delited KAR file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$ORIG_CACHE_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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1457
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<pre style="margin: 0;">+<span id="LC1457" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1458
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<pre style="margin: 0;">+<span id="LC1458" class="line" lang="shell"></span>
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1459
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<pre style="margin: 0;">+<span id="LC1459" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NEW_CACHE_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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1460
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<pre style="margin: 0;">+<span id="LC1460" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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1461
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<pre style="margin: 0;">+<span id="LC1461" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat</span> .VDBCACHE <span class="k" style="font-weight: 600;">for </span>delited KAR file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$NEW_CACHE_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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1462
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<pre style="margin: 0;">+<span id="LC1462" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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1463
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<pre style="margin: 0;">+<span id="LC1463" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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1465
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<pre style="margin: 0;">+<span id="LC1465" class="line" lang="shell"></span>
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1466
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<pre style="margin: 0;">+<span id="LC1466" class="line" lang="shell">test_proc <span class="o" style="font-weight: 600;">()</span></span>
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1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="shell"><span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1468
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<pre style="margin: 0;">+<span id="LC1468" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">## checking if it is was delited</span></span>
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1469
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<pre style="margin: 0;">+<span id="LC1469" class="line" lang="shell"> check_ready_for_test</span>
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1470
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<pre style="margin: 0;">+<span id="LC1470" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1471
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<pre style="margin: 0;">+<span id="LC1471" class="line" lang="shell"> info_msg Changing directory to <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$TARGET_DIR</span><span class="se" style="color: #d14;">\'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1472
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<pre style="margin: 0;">+<span id="LC1472" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$TARGET_DIR</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1473
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<pre style="margin: 0;">+<span id="LC1473" class="line" lang="shell"></span>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1474
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<pre style="margin: 0;">+<span id="LC1474" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VDBCFG_NAME</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1475
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<pre style="margin: 0;">+<span id="LC1475" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>dpec__ 105<span class="p">;</span> err_exit can not <span class="nb" style="color: #0086b3;">stat </span>file <span class="se" style="color: #d14;">\'</span><span class="nv" style="color: #008080;">$VDBCFG_FILE</span><span class="se" style="color: #d14;">\'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1478
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<pre style="margin: 0;">+<span id="LC1478" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>test_kar</span>
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<td class="diff-line-num new new_line" data-linenumber="1480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="shell"></span>
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1481
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<pre style="margin: 0;">+<span id="LC1481" class="line" lang="shell"> info_msg <span class="s2" style="color: #d14;">"DONE"</span></span>
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1482
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<pre style="margin: 0;">+<span id="LC1482" class="line" lang="shell"><span class="o" style="font-weight: 600;">}</span></span>
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1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="shell"></span>
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1373
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<td class="diff-line-num new_line" data-linenumber="1484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###############################################################################################</span></span>
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1374
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<td class="diff-line-num new_line" data-linenumber="1485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###############################################################################################</span></span>
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1375
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1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">###<<>>### Status</span></span>
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