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<h3>
Shruti Sridhar pushed to branch master
at <a href="https://salsa.debian.org/med-team/daligner">Debian Med / daligner</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/a189ea945628fb709bbbfa311b6c77222946eafd">a189ea94</a></strong>
<div>
<span>by Shruti Sridhar</span>
<i>at 2020-08-12T20:18:06+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">added autopkgtests
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/64bebc730ba7cd8ade0bc27331b6485cf9ae34ab">64bebc73</a></strong>
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<span>by Shruti Sridhar</span>
<i>at 2020-08-12T20:19:07+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install docs
</pre>
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<h4>4 changed files:</h4>
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<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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debian/README.test
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/daligner/-/compare/d21f1ee257a2ce3982a84e44c3c8a9f63b33b921...64bebc730ba7cd8ade0bc27331b6485cf9ae34ab#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<a href="https://salsa.debian.org/med-team/daligner/-/compare/d21f1ee257a2ce3982a84e44c3c8a9f63b33b921...64bebc730ba7cd8ade0bc27331b6485cf9ae34ab#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.*</span></pre>
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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">\ No newline at end of file</td>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/daligner/-/compare/d21f1ee257a2ce3982a84e44c3c8a9f63b33b921...64bebc730ba7cd8ade0bc27331b6485cf9ae34ab#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-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @,dazzdb, @,tcsh</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="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/daligner/-/compare/d21f1ee257a2ce3982a84e44c3c8a9f63b33b921...64bebc730ba7cd8ade0bc27331b6485cf9ae34ab#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>daligner</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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7
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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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"</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;">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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">rangen 1.0 <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span>R.fasta </span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">fasta2DAM R R.fasta </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">dsimulator R <span class="nt" style="color: #000080;">-c20</span><span class="nb" style="color: #0086b3;">.</span> <span class="nt" style="color: #000080;">-r2020</span> <span class="o" style="font-weight: 600;">></span>G.fasta </span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">fasta2DB G G.fasta </span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm </span>G.fasta </span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell">DBsplit <span class="nt" style="color: #000080;">-s11</span> G </span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">DBdust G.1 </span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">DBdust G.2 </span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">DBstats <span class="nt" style="color: #000080;">-mdust</span> G </span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>G.db</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">HPC.daligner <span class="nt" style="color: #000080;">-mdust</span> <span class="nt" style="color: #000080;">-t5</span> G | tcsh <span class="nt" style="color: #000080;">-v</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">LAshow <span class="nt" style="color: #000080;">-c</span> G <span class="nt" style="color: #000080;">-w50</span> G.1 | <span class="nb" style="color: #0086b3;">head</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Since the output is not consistent.</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#It cannot be compared with the reference. </span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span></pre>
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