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<h3>
Saira Hussain pushed to branch master
at <a href="https://salsa.debian.org/med-team/norsnet">Debian Med / norsnet</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/norsnet/commit/a582802b5885b8e9b6d76cc234b67a310ab30680">a582802b</a></strong>
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<span>by Saira Hussain</span>
<i>at 2019-07-31T10:31:25Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add basic test functionality
</pre>
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<strong><a href="https://salsa.debian.org/med-team/norsnet/commit/8e8064ec462d3e8706dc05de0ebd805c824a3477">8e8064ec</a></strong>
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<span>by Saira Hussain</span>
<i>at 2019-07-31T10:33:00Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Bump changelog
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<h4>4 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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debian/examples
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debian/tests/control
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debian/tests/run-unit-tests
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/norsnet/compare/bbd49b7bfaef84ca1cea23383129893a16d1617d...8e8064ec462d3e8706dc05de0ebd805c824a3477#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">norsnet (1.0.17-5) UNRELEASED; 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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [Saira Hussain]</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add unit tests</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Saira Hussain <saira.h0213@zoho.com> Wed, 31 Jul 2019 11:31:56 +0100</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">norsnet (1.0.17-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * pp-popularity-contest only suggested</span>
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<li id="9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<a href="https://salsa.debian.org/med-team/norsnet/compare/bbd49b7bfaef84ca1cea23383129893a16d1617d...8e8064ec462d3e8706dc05de0ebd805c824a3477#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">examples/*</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/norsnet/compare/bbd49b7bfaef84ca1cea23383129893a16d1617d...8e8064ec462d3e8706dc05de0ebd805c824a3477#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-tests</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<li id="b8880ead45e8d099a1552defb95ea70479f1572e">
<a href="https://salsa.debian.org/med-team/norsnet/compare/bbd49b7bfaef84ca1cea23383129893a16d1617d...8e8064ec462d3e8706dc05de0ebd805c824a3477#b8880ead45e8d099a1552defb95ea70479f1572e"><strong>debian/tests/run-unit-tests</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>mcl</span>
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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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<pre style="margin: 0;">+<span id="LC6" 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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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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8
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<pre style="margin: 0;">+<span id="LC8" 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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Just for debugging</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Generation of protein families</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">mcxload <span class="nt" style="color: #000080;">-abc</span> protein_graphs.txt <span class="nt" style="color: #000080;">--stream-mirror</span> <span class="nt" style="color: #000080;">--stream-neg-log10</span> <span class="nt" style="color: #000080;">-stream-tf</span> <span class="s1" style="color: #d14;">'ceil(200)'</span> <span class="nt" style="color: #000080;">-o</span> protein_graphs.mci <span class="nt" style="color: #000080;">-write-tab</span> protein_graphs.tab</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">mcl protein_graphs.mci <span class="nt" style="color: #000080;">-I</span> 2</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">mcxdump <span class="nt" style="color: #000080;">-icl</span> out.protein_graphs.mci.I20 <span class="nt" style="color: #000080;">-tabr</span> protein_graphs.tab <span class="nt" style="color: #000080;">-o</span> clusters.protein_graphs.mci.I20</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Building clusters of genomes</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">mcxload <span class="nt" style="color: #000080;">-abc</span> genome_graphs.txt <span class="nt" style="color: #000080;">--stream-mirror</span> <span class="nt" style="color: #000080;">-o</span> genome_graphs.mci <span class="nt" style="color: #000080;">-write-tab</span> genome_graphs.tab</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">mcl genome_graphs.mci <span class="nt" style="color: #000080;">-I</span> 1.2</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">mcl genome_graphs.mci <span class="nt" style="color: #000080;">-I</span> 2</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell">mcl genome_graphs.mci <span class="nt" style="color: #000080;">-I</span> 4</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell">mcl genome_graphs.mci <span class="nt" style="color: #000080;">-I</span> 6</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell">mcxdump <span class="nt" style="color: #000080;">-icl</span> out.genome_graphs.mci.I12 <span class="nt" style="color: #000080;">-tabr</span> genome_graphs.tab <span class="nt" style="color: #000080;">-o</span> clusters.genome.mci.I12</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">mcxdump <span class="nt" style="color: #000080;">-icl</span> out.genome_graphs.mci.I20 <span class="nt" style="color: #000080;">-tabr</span> genome_graphs.tab <span class="nt" style="color: #000080;">-o</span> clusters.genome.mci.I20</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell">mcxdump <span class="nt" style="color: #000080;">-icl</span> out.genome_graphs.mci.I40 <span class="nt" style="color: #000080;">-tabr</span> genome_graphs.tab <span class="nt" style="color: #000080;">-o</span> clusters.genome.mci.I40</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">mcxdump <span class="nt" style="color: #000080;">-icl</span> out.genome_graphs.mci.I60 <span class="nt" style="color: #000080;">-tabr</span> genome_graphs.tab <span class="nt" style="color: #000080;">-o</span> clusters.genome.mci.I60</span></pre>
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