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<h3>
Andreas Tille 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/c99b53a13c709ea888b204c2d8ce3d33602010a6">c99b53a1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-12T22:53:10+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add changes to changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/676ce9ed1adfc0349581ecbf9e664ff9c40c3feb">676ce9ed</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-12T22:53:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">'@' is the variable for the actual binary packages build from the source package. It is needed only once
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/c72457e68c5214b4d394cb07c5cec30adcb2f8dd">c72457e6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-12T22:55:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unneeded comments from boilerplate
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/c90b68ea31d45b1e57f02832418c85fdf4f7f99d">c90b68ea</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-13T08:57:27+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install run-unit-test script to serve as a user example
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/d15fb6659b60a52e6b6b72518cb43ff4fb1df0e2">d15fb665</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-13T08:58:06+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not unnecessarily depend from csh
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/694f2e453b7962151dc952906faa21a4f665dcc9">694f2e45</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-13T08:58:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Make sure users who want to run the autopkgtest as example will know that it needs dazzdb
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/daligner/-/commit/a2f2a7aa105ef02f929e59577361ecf3f2cc050c">a2f2a7aa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-08-13T09:10:21+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
debian/README.test
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/daligner/-/compare/64bebc730ba7cd8ade0bc27331b6485cf9ae34ab...a2f2a7aa105ef02f929e59577361ecf3f2cc050c#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" 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">@@ -3,6 +3,7 @@ Notes on how this package can be tested.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new_line" data-linenumber="4" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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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<td class="diff-line-num new_line" data-linenumber="5" 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">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sudo</span> <span class="nx">apt</span> <span class="nx">install</span> <span class="nx">dazzdb</span></span>
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<td class="diff-line-num new_line" data-linenumber="7" 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">
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<pre style="margin: 0;"> <span id="LC7" 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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<td class="diff-line-num new_line" data-linenumber="8" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"></span>
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<td class="diff-line-num new_line" data-linenumber="9" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" 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="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/daligner/-/compare/64bebc730ba7cd8ade0bc27331b6485cf9ae34ab...a2f2a7aa105ef02f929e59577361ecf3f2cc050c#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">daligner (1.0+git20200727.ed40ce5-2) unstable; 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"> * added autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Install docs</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Shruti Sridhar <shruti.sridhar99@gmail.com> Wed, 12 Aug 2020 22:52:11 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">daligner (1.0+git20200727.ed40ce5-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/README.*</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/daligner/-/compare/64bebc730ba7cd8ade0bc27331b6485cf9ae34ab...a2f2a7aa105ef02f929e59577361ecf3f2cc050c#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: @,<span class="idiff left right">dazzdb, @,tcsh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @,<span class="idiff left right"> dazzdb</span></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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<a href="https://salsa.debian.org/med-team/daligner/-/compare/64bebc730ba7cd8ade0bc27331b6485cf9ae34ab...a2f2a7aa105ef02f929e59577361ecf3f2cc050c#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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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">@@ -9,11 +9,8 @@ if [ "${AUTOPKGTEST_TMP}" = "" ] ; then</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</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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<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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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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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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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC12" 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="LC13" class="line" lang="shell"></span>
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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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<pre style="margin: 0;"> <span id="LC14" 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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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">fasta2DAM R R.fasta </span>
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<pre style="margin: 0;"> <span id="LC16" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,10 +21,9 @@ DBdust G.1</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell">DBdust G.2 </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell">DBstats <span class="nt" style="color: #000080;">-mdust</span> G </span>
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<pre style="margin: 0;"> <span id="LC23" 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 class="idiff left right"> </span></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 | <span class="idiff left right">tc</span>sh <span class="nt" style="color: #000080;">-v</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">HPC.daligner <span class="nt" style="color: #000080;">-mdust</span> <span class="nt" style="color: #000080;">-t5</span> G | sh <span class="nt" style="color: #000080;">-v</span></span>
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29
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<pre style="margin: 0;"> <span id="LC26" 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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30
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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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31
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<pre style="margin: 0;"> <span id="LC28" 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="LC29" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#It cannot be compared with the reference. </span></span></pre>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"></span></pre>
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