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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/97769cd4143ff22346788786b52dc24ae276bbd8">97769cd4</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2020-07-02T21:05:37+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add test data and write some autopkgtest
</pre>
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
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+
debian/source/include-binaries
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<li class="file-stats">
<a href="#bf1e729e892e70458d50e5467c62bb369798ff20">
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+
debian/tests/ecoli_config_file.txt
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<li class="file-stats">
<a href="#5f5b82885d994776408e148d26e9f6232f670362">
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+
debian/tests/ecoli_filtered.fastq.gz
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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="d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/97769cd4143ff22346788786b52dc24ae276bbd8#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</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">debian/tests/ecoli_filtered.fastq.gz</span>
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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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/ecoli_config_file.txt</span></pre>
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</li>
<li id="bf1e729e892e70458d50e5467c62bb369798ff20">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/97769cd4143ff22346788786b52dc24ae276bbd8#bf1e729e892e70458d50e5467c62bb369798ff20"><strong>debian/tests/ecoli_config_file.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">PROJECT=ecoli</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RAWREADS=ecoli_filtered.fastq</span>
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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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">GENOME_SIZE=4800000</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">THREADS=4</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">MIN_READ_LENGTH=2000</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">CNS_OVLP_OPTIONS="-kmer_size 13"</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">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">CNS_PCAN_OPTIONS="-p 100000 -k 100"</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">CNS_OPTIONS=""</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">CNS_OUTPUT_COVERAGE=30</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">TRIM_OVLP_OPTIONS="-skip_overhang"</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">TRIM_PM4_OPTIONS="-p 100000 -k 100"</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">TRIM_LCR_OPTIONS=""</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">TRIM_SR_OPTIONS=""</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="plaintext">ASM_OVLP_OPTIONS=""</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="plaintext">FSA_OL_FILTER_OPTIONS="--max_overhang=-1 --min_identity=-1"</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="plaintext">FSA_ASSEMBLE_OPTIONS=""</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">CLEANUP=0</span></pre>
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<li id="5f5b82885d994776408e148d26e9f6232f670362">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/97769cd4143ff22346788786b52dc24ae276bbd8#5f5b82885d994776408e148d26e9f6232f670362"><strong>debian/tests/ecoli_filtered.fastq.gz</strong></a>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/mecat2/-/commit/97769cd4143ff22346788786b52dc24ae276bbd8#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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 class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="c" style="color: #998; font-style: italic;">#PACKAGENAME#</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"></span>
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6
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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5
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<pre style="margin: 0;"> <span id="LC5" 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="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,8 +10,16 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</td>
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12
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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;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> debian/tests/ecoli_filtered.fastq.gz debian/tests/ecoli_config_file.txt <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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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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17
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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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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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span></pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Extract the test data</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip </span>ecoli_filtered.fastq.gz</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Trim out low quality subsequences in corrected reads</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">mecat trim ecoli_config_file.txt</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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<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></pre>
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