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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/c9ecc36cac78883c1b0506a06faa89b5e9962e5f">c9ecc36c</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-02-04T20:34:44-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Start work on sra-sdk 2.10.9+dfsg-2.
</pre>
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<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/0477964a2345ccef626295faa66594f184ac114a">0477964a</a></strong>
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<span>by Aaron M. Ucko</span>
<i>at 2021-02-04T20:35:54-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">run-unit-test: Give up for now on {abi,fastq,illumina,sff}-load.
All four rely deeply on retired VDB functionality that would be
too awkward to reintroduce.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/7a202959ed79f11d635a2db371057336cc0e7296">7a202959</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-02-04T20:38:06-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New patch skip_broken_loaders.patch.
Stop building or trying to install anything from tools/sra-load, to
avoid leading users on.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sra-sdk/-/commit/4acc0f4f33ac4766b969f89b46a91307874faa67">4acc0f4f</a></strong>
<div>
<span>by Aaron M. Ucko</span>
<i>at 2021-02-04T20:38:52-05:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Finalize sra-sdk 2.10.9+dfsg-2 for unstable.
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#7db49031ef1dec8bcaa2bf64082d573e6230e36b">
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+
debian/patches/skip_broken_loaders.patch
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/63cf3ac188e9e2157270764a1350af3296c324bb...4acc0f4f33ac4766b969f89b46a91307874faa67#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sra-sdk (2.10.9+dfsg-2) 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"> * run-unit-test: Give up for now on {abi,fastq,illumina,sff}-load.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> All four rely deeply on retired VDB functionality that would be</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> too awkward to reintroduce.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * skip_broken_loaders.patch (new): Likewise stop building or trying to</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> install anything from tools/sra-load, to avoid leading users on.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Aaron M. Ucko <ucko@debian.org> Thu, 04 Feb 2021 20:38:51 -0500</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">sra-sdk (2.10.9+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/63cf3ac188e9e2157270764a1350af3296c324bb...4acc0f4f33ac4766b969f89b46a91307874faa67#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<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">@@ -20,3 +20,4 @@ python3</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">use_exposed_headers.patch</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">use_unversioned_tools.patch</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">#reenable_legacy_schema_in_sra_load.patch</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">skip_broken_loaders.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/63cf3ac188e9e2157270764a1350af3296c324bb...4acc0f4f33ac4766b969f89b46a91307874faa67#7db49031ef1dec8bcaa2bf64082d573e6230e36b"><strong>debian/patches/skip_broken_loaders.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tools/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tools/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -60,7 +60,6 @@</span> SUBDIRS = \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> vcf-loader \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> copycat \</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> fasterq-dump \</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sra-load \</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> ccextract \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> pacbio-load \</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> fuse \</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;">--- a/build/Makefile.install</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build/Makefile.install</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span> include $(TOP)/build/Makefile.$(OS)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> include $(TOP)/build/Makefile.tools</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> ifeq (1,$(HAVE_HDF5))</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> TOOLS_TO_COPY += pacbio-load</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- TOOLS_TO_COPY += pacbio-loadxml</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ TOOLS_TO_COPY_OPTIONAL += pacbio-loadxml</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> endif</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> # unset outside defined variables</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/sra-sdk/-/compare/63cf3ac188e9e2157270764a1350af3296c324bb...4acc0f4f33ac4766b969f89b46a91307874faa67#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="46" 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">@@ -46,18 +46,18 @@ latf-load -p LS454 --quality PHRED_33 -o SRR2042184 SRR2042184_1.fastq</td>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running kar..."</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="shell">kar <span class="nt" style="color: #000080;">-c</span> SRR2042184.sra <span class="nt" style="color: #000080;">-d</span> SRR2042184</span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> SRR2042184.sra <span class="o" style="font-weight: 600;">]</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running fastq-load..."</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="shell">fastq-load <span class="nt" style="color: #000080;">-r</span> meta/SRR6650398_fastq_run.xml <span class="nt" style="color: #000080;">-e</span> meta/SRR6650398_experiment.xml <span class="nt" style="color: #000080;">-o</span> SRR6650398</span>
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<td class="diff-line-num old old_line" data-linenumber="51" 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">
51
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<td class="diff-line-num new_line old" data-linenumber="49" 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="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> SRR2042184 SRR6650398 SRR2042184.sra SRR2042184_1.fastq SRR6650398_1.fastq</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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 class="idiff left right"># </span>echo ">>>>>Running fastq-load..."</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="52" style="width: 35px; color: rgba(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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;"><span class="idiff left right"># </span>fastq-load -r meta/SRR6650398_fastq_run.xml -e meta/SRR6650398_experiment.xml -o SRR6650398</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r<span class="idiff left right">f</span></span> SRR2042184 SRR6650398 SRR2042184.sra SRR2042184_1.fastq SRR6650398_1.fastq</span>
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52
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<td class="diff-line-num new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="shell"></span>
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<td class="diff-line-num old_line" data-linenumber="53" 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">
53
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<td class="diff-line-num new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running abi-dump..."</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="54" 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">
54
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<td class="diff-line-num new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="shell">abi-dump <span class="nt" style="color: #000080;">-F</span> SRR7032226</span>
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<td class="diff-line-num old_line" data-linenumber="55" 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">
55
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<td class="diff-line-num new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># make sequence descriptor to look like from SOLiD</span></span>
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<td class="diff-line-num old_line" data-linenumber="56" 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">
56
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<td class="diff-line-num new_line" data-linenumber="56" 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">
56
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/>1/>1_11_1111_F3/'</span> SRR7032226_F3.csfasta <span class="o" style="font-weight: 600;">></span> SRR7032226_F3e.csfasta</span>
</pre>
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57
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<td class="diff-line-num new_line" data-linenumber="57" 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">
57
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/>1/>1_11_1111_F3/'</span> SRR7032226_F3_QV.qual <span class="o" style="font-weight: 600;">></span> SRR7032226_F3_QVe.qual</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="58" 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">
58
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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running abi-load..."</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="59" 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">
59
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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC59" class="line" lang="shell">abi-load <span class="nt" style="color: #000080;">-r</span> meta/SRR7032226_run.xml <span class="nt" style="color: #000080;">-e</span> meta/SRR7032226_experiment.xml <span class="nt" style="color: #000080;">-o</span> SRR7032226</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="60" 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">
60
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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r</span> SRR7032226 SRR7032226_F3<span class="k" style="font-weight: 600;">*</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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 class="idiff left right"># </span>echo ">>>>>Running abi-load..."</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;"><span class="idiff left right"># </span>abi-load -r meta/SRR7032226_run.xml -e meta/SRR7032226_experiment.xml -o SRR7032226</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r<span class="idiff left right">f</span></span> SRR7032226 SRR7032226_F3<span class="k" style="font-weight: 600;">*</span></span>
</pre>
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61
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="62" 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">
62
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<td class="diff-line-num new_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running sam-dump..."</span></span>
</pre>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="shell">sam-dump <span class="nt" style="color: #000080;">--output-file</span> SRR6650398.sam SRR6650398</span>
</pre>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,14 +67,14 @@ rm -r SRR6650398 SRR6650398.sam</td>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="68" 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">
68
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<td class="diff-line-num new_line" data-linenumber="68" 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">
68
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running illumina-dump..."</span></span>
</pre>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="shell">illumina-dump <span class="nt" style="color: #000080;">--qseq</span> 1 SRR6650398</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running illumina-load..."</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="shell">illumina-load <span class="nt" style="color: #000080;">-r</span> meta/SRR6650398_illumina_run.xml <span class="nt" style="color: #000080;">-e</span> meta/SRR6650398_experiment.xml <span class="nt" style="color: #000080;">-o</span> SRR6650398</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;">rm</span> <span class="nt" style="color: #000080;">-r</span> SRR6650398 SRR6650398_0_0001_qseq.txt</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>echo ">>>>>Running illumina-load..."</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>illumina-load -r meta/SRR6650398_illumina_run.xml -e meta/SRR6650398_experiment.xml -o SRR6650398</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-r<span class="idiff left right">f</span></span> SRR6650398 SRR6650398_0_0001_qseq.txt</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="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running sff-dump..."</span></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="shell">sff-dump SRR2042184</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running sff-load..."</span></span>
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<td class="diff-line-num old old_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="shell">sff-load <span class="nt" style="color: #000080;">-r</span> meta/SRR2042184_run.xml <span class="nt" style="color: #000080;">-e</span> meta/SRR2042184_experiment.xml <span class="nt" style="color: #000080;">-o</span> SRR2042184</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">
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>echo ">>>>>Running sff-load..."</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>sff-load -r meta/SRR2042184_run.xml -e meta/SRR2042184_experiment.xml -o SRR2042184</span></span>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"></span>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">">>>>>Running vdb-dump..."</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell">vdb-dump <span class="nt" style="color: #000080;">-f</span> tab <span class="nt" style="color: #000080;">-C</span> READ SRR2042184 | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'{print ">" "SRR2042184." NR "\n" $0}'</span> <span class="o" style="font-weight: 600;">></span> SRR2042184.fasta</span>
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