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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/discosnp">Debian Med / discosnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/45dc3905d4096798cbb42bd1f9b618c61dad26ee">45dc3905</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T15:46:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not tweak Python3 interpreter in d/rules once this was done properly in a patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/38b49ece173114394a331edad78fe2f30f7d8d52">38b49ece</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T15:52:34+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix POSIX shell syntax
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/d74c12121cd976881f9a383e3a84ae5e95343e9f">d74c1212</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T15:53:16+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">discoSnpRAD is a dir with extra scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/f56c821ba2b791565d66785376b9f8799caa9528">f56c821b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T15:55:26+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt to new names
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/bbd033a4aba4bde6a05071014596b5e8c1e6a8a0">bbd033a4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T15:59:17+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6">30cd3f3d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T16:02:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
</a>
</li>
<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
debian/lintian-overrides
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#7221a1667ed3ab6815deb533432820f5525a0187">
<span class="new-file">
+
debian/patches/shell_syntax.patch
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</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">discosnp (2.4.3-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">discosnp (2.4.3-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></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="plaintext"> [ Steffen Moeller ]</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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="4" 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="LC4" class="line" lang="plaintext"> * New upstream version</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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ discosnp (2.4.3-1) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog (routine-update)</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository.</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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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 27 Jan 2020 1<span class="idiff left right">4:14:13</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 27 Jan 2020 1<span class="idiff left right">5:59:28</span> +0100</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">discosnp (2.3.0-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<li id="68d8c5c6babbf5cf109b2584c454449dbff75772">
<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">scripts usr/share/discosnp</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">discoSnpRAD usr/share/discosnp</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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">run_discoSnp*.sh usr/bin</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">discoSnpRAD usr/bin</span></pre>
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<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">discosnp: script-with-language-extension usr/bin/run_discoSnp++.sh</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">discosnp: script-with-language-extension usr/bin/run_discoSnpRad.sh</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">discosnp: script-with-language-extension usr/bin/run_*.sh</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># The doc is where it belongs to</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/<span class="idiff left right">scripts_RAD</span>/README.md</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">discosnp: package-contains-documentation-outside-usr-share-doc usr/share/discosnp/<span class="idiff left right">*</span>/README.md</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -5,3 +5,4 @@ spelling.patch</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">#fix_scripts.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">adapt_test_scripts.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">2to3.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">shell_syntax.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#7221a1667ed3ab6815deb533432820f5525a0187"><strong>debian/patches/shell_syntax.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Mon, 27 Jan 2020 15:51:58 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix POSIX shell syntax</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/discoSnpRAD/clustering_scripts/discoRAD_clustering.sh</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span> bold=`tput bold`</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> reset=`tput sgr0`</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-function help {</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+help() {</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> echo $reset</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> echo "====================================================="</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> echo "Filtering, clustering per locus and vcf formatting of $rawdiscofile"</span></pre>
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<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,9 +15,6 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/bin/read_file_names debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/bin/quick_hierarchical_clustering debian/$(DEB_SOURCE)/usr/lib/$(DEB_SOURCE)/bin</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> rm -rf debian/$(DEB_SOURCE)/usr/share/discosnp/scripts/jenkins</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> for pl in `grep -Rl -e '#![[:space:]]*/bin/python' -e '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> sed -i '1s?^#!.*python?#!/usr/bin/python3?' $${pl} ; \</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> done</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> dh_installman</span>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/discosnp/compare/b036b8fc05bc73546ea6c10a2396b53654e439d1...30cd3f3dc7369cdf3b729b97978758ecb1fdd5a6#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test/<span class="k" style="font-weight: 600;">*</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip </span>ref_<span class="idiff left">discoRes_k_31_c_auto_D_100_P_1_b_0_coherent</span><span class="k" style="font-weight: 600;"><span class="idiff right">*</span></span>.gz</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip </span>ref_<span class="k" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="idiff right">.fa</span>.gz</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod</span> +x simple_test.sh</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell">./simple_test.sh</span></pre>
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