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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/megahit">Debian Med / megahit</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/megahit/commit/39fac62663cad276a5e17cee1f34e7f06baee4d9">39fac626</a></strong>
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<span>by Shayan Doust</span>
<i>at 2019-10-17T21:36:50Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest
Temp remove the patch for the source fix (pbuilder failed) as this is problematic
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<h4>2 changed files:</h4>
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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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="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/megahit/commit/39fac62663cad276a5e17cee1f34e7f06baee4d9#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_test_path.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">2to3.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">fix_src_packed_field.patch</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/megahit/commit/39fac62663cad276a5e17cee1f34e7f06baee4d9#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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<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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"></span>
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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;"><span class="idiff left right">#PACKAGENAME#</span></span></span>
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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="idiff left right">megahit</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC6" 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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<pre style="margin: 0;"> <span id="LC7" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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<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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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="idiff left right">examples</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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<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> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/<span class="idiff left right">data</span>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" 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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip </span>r3_1.fa.gz r3_2.fa.gz</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">megahit <span class="nt" style="color: #000080;">--test</span> <span class="nt" style="color: #000080;">-t</span> 2</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">MEGAHIT_NUM_MERCY_FACTOR</span><span class="o" style="font-weight: 600;">=</span>1.5 megahit <span class="nt" style="color: #000080;">--test</span> <span class="nt" style="color: #000080;">-t</span> 4 <span class="nt" style="color: #000080;">--mem-flag</span> 0 <span class="nt" style="color: #000080;">--no-hw-accel</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">megahit <span class="nt" style="color: #000080;">--test</span> <span class="nt" style="color: #000080;">-t</span> 2 <span class="nt" style="color: #000080;">--kmin-1pass</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> test-random <span class="o" style="font-weight: 600;">&&</span> python3 generate_random_fasta.py <span class="o" style="font-weight: 600;">></span> random.fa <span class="o" style="font-weight: 600;">&&</span> megahit <span class="nt" style="color: #000080;">-r</span> random.fa <span class="nt" style="color: #000080;">--k-list</span> 255 <span class="nt" style="color: #000080;">--min-count</span> 1 <span class="nt" style="color: #000080;">-o</span> test-random</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> test-fastg <span class="o" style="font-weight: 600;">&&</span> megahit <span class="nt" style="color: #000080;">--test</span> <span class="nt" style="color: #000080;">-t</span> 2 <span class="nt" style="color: #000080;">--mem-flag</span> 2 <span class="nt" style="color: #000080;">--keep-tmp-files</span> <span class="nt" style="color: #000080;">-o</span> test-fastg</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">megahit_toolkit contig2fastg 59 test-fastg/intermediate_contigs/k59.contigs.fa <span class="o" style="font-weight: 600;">></span> 59.fastg</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">megahit_toolkit readstat < test-fastg/intermediate_contigs/k59.contigs.fa</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"></span></pre>
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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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