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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/mecat2">Debian Med / mecat2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mecat2/-/commit/a72a0409243b5d21479262fd14728f55c3342480">a72a0409</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-07-03T14:55:21+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Write autopkgtest
</pre>
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<h4>1 changed file:</h4>
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/a72a0409243b5d21479262fd14728f55c3342480#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -23,3 +23,20 @@ mecat trim ecoli_config_file.txt</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"></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;"># Assemble contigs using the trimmed reads</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell">mecat assemble ecoli_config_file.txt</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;"># Now, at least check that we have the resulted files and they have something in them</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">CORRECTED_READS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"ecoli/1-consensus/cns_reads_list.txt"</span></span>
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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;">CORRECTED_READS_TRIMMING</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"ecoli/1-consensus/cns_final.fasta"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nv" style="color: #008080;">TRIMMED_READS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"ecoli/2-trim_bases/trimReads.fasta"</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nv" style="color: #008080;">ASSEMBLED_CONTIGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"ecoli/4-fsa/contigs.fasta"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>FILE <span class="k" style="font-weight: 600;">in</span> <span class="nv" style="color: #008080;">$CORRECTED_READS</span> <span class="nv" style="color: #008080;">$CORRECTED_READS_TRIMMING</span> <span class="nv" style="color: #008080;">$TRIMMED_READS</span> <span class="nv" style="color: #008080;">$ASSEMBLED_CONTIGS</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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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="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-s</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"[FAIL] </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;"> should have data in it, but doesn't or the file doesn't exist."</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC40" 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;">"[PASS] </span><span class="nv" style="color: #008080;">$FILE</span><span class="s2" style="color: #d14;"> exists and has data in it."</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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