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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/4ae2b5be9438b15309cefc45821053fde23f80e0">4ae2b5be</a></strong>
<div>
<span>by Saira Hussain</span>
<i>at 2019-07-31T10:37:09Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add shipped in example data files to test
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<h4>1 changed file:</h4>
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<a href="#b8880ead45e8d099a1552defb95ea70479f1572e">
debian/tests/run-unit-tests
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<h4>Changes:</h4>
<li id="b8880ead45e8d099a1552defb95ea70479f1572e">
<a href="https://salsa.debian.org/med-team/norsnet/commit/4ae2b5be9438b15309cefc45821053fde23f80e0#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><span class="idiff left right">mcl</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">norsnet</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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<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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,22 +19,8 @@ gunzip -r *</td>
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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;">#<span class="idiff left right">Generation of protein famili</span>es</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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="LC23" class="line" lang="shell"><span class="idiff left">mcxload </span><span class="nt" style="color: #000080;"><span class="idiff">-abc</span></span><span class="idiff"> protein_graphs.txt </span><span class="nt" style="color: #000080;"><span class="idiff">--stream-mirror</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">--stream-neg-log10</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-stream-tf</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'ceil(200)'</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-o</span></span><span class="idiff"> protein_graphs.mci </span><span class="nt" style="color: #000080;"><span class="idiff">-write-tab</span></span><span class="idiff right"> protein_graphs.tab</span></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;">#<span class="idiff left right"> Run the shipped example data fil</span>es</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="idiff left right">norsnet cad23.f cad23-fil.rdbProf cad23-fil.hssp cad23.norsnet cad23 cad23.profbval</span></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="LC25" 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="LC26" class="line" lang="shell"></span></pre>
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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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