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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/kmer">Debian Med / kmer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250">e910a4d3</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-08-20T08:09:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
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<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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+
debian/README.test
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</li>
<li class="file-stats">
<a href="#88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c">
debian/atac.docs
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#f83de6c204fa5f0197ff393cb6b4dd851dc482d7">
debian/sim4db.docs
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<li class="file-stats">
<a href="#8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058">
debian/tests/atac-unit-test
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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</li>
<li class="file-stats">
<a href="#250298e80304390409b063185886417f177a00db">
<span class="new-file">
+
debian/tests/sim4db-unit-test
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</li>
<li class="file-stats">
<a href="#9abb8ed09a0cbe2f2cce9c00629715155e9493b4">
debian/tests/test-data/test_data.tar.gz
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#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">the</span> <span class="nx">packages</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">their</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" 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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">____________________________________________________________________________</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">To</span> <span class="nx">test</span> <span class="nx">atac</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">atac</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">NOTE</span><span class="o" style="font-weight: 600;">:</span> <span class="nx">Atac</span> <span class="nx">test</span> <span class="nx">fails</span> <span class="nx">with</span> <span class="nx">a</span> <span class="nx">segmentation</span> <span class="nx">fault</span><span class="o" style="font-weight: 600;">.</span> <span class="nx">Feel</span> <span class="nx">free</span> <span class="nx">to</span> <span class="k" style="font-weight: 600;">use</span> <span class="sb" style="color: #d14;">`reportbug</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="sb" style="color: #d14;">atac`</span> <span class="k" style="font-weight: 600;">if</span> <span class="nx">you</span> <span class="nx">have</span> <span class="nx">some</span> <span class="nx">idea</span> <span class="nx">how</span> <span class="nx">to</span> <span class="nx">fix</span> <span class="nx">the</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">.</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="11" 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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"><span class="nx">To</span> <span class="nx">test</span> <span class="nx">sim4db</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">:</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">sim4db</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="LC14" class="line" lang="php"></span></pre>
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<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c"><strong>debian/atac.docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.atac</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/tests/atac-unit-test</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">debian/tests/test-data/test_data.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/README.test</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kmer (0~20150903+r2013-5) UNRELEASED; urgency=medium</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"> * Add autopkgtest.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Mon, 20 Aug 2018 09:46:55 +0200</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">kmer (0~20150903+r2013-4) unstable; urgency=medium</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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -36,6 +36,24 @@ Copyright:</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> 2015-2016 Afif Elghraoui <afif@debian.org></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">License: GPL-2+</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Files: debian/tests/test-data/test_data.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Copyright: 1996-2018 NCBI</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">License: unrestricted</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> Databases of molecular data on the NCBI Web site include such examples as</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> nucleotide sequences (GenBank), protein sequences, macromolecular</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> structures, molecular variation, gene expression, and mapping data. They</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> are designed to provide and encourage access within the scientific</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> community to sources of current and comprehensive information. Therefore,</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> NCBI itself places no restrictions on the use or distribution of the data</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> contained therein. Nor do we accept data when the submitter has requested</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> restrictions on reuse or redistribution.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> The test data files contained in the archive were downloaded from NCBI RefSeq</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> and EST databases using wget and idfetch (from ncbi-tools-bin package):</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/latest_assembly_versions/GCF_000195955.2_ASM19595v2/GCF_000195955.2_ASM19595v2_genomic.fna.gz</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_leprae/latest_assembly_versions/GCF_000195855.1_ASM19585v1/GCF_000195855.1_ASM19585v1_genomic.fna.gz</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> idfetch -G EST_GIs.txt -t 5 -o ESTs.fasta</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">License: GPL-2+</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#f83de6c204fa5f0197ff393cb6b4dd851dc482d7"><strong>debian/sim4db.docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.sim4db</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/sim4db-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/tests/test-data/test_data.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/README.test</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">@@ -7,9 +7,15 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</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="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;"><span class="idiff left">-a</span></span><span class="idiff right"> </span>/usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test_data.tar.gz <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test_data.tar.gz <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xzvf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz</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="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run atac:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell">atac <span class="nt" style="color: navy;">-meryldir</span> meryldir <span class="nt" style="color: navy;">-dir</span> results <span class="nt" style="color: navy;">-id1</span> Ecoli <span class="nt" style="color: navy;">-seq1</span> GCF_000195995.1_ASM19599v1_genomic.fna <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"> <span class="nt" style="color: navy;">-id2</span> Sent <span class="nt" style="color: navy;">-seq2</span> GCF_000005845.2_ASM584v2_genomic.fna</span></pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">atac <span class="nt" style="color: navy;">-meryldir</span> meryldir <span class="nt" style="color: navy;">-dir</span> results <span class="nt" style="color: navy;">-id1</span> Lepr <span class="nt" style="color: navy;">-seq1</span> GCF_000195855.1_ASM19585v1_genomic.fna <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"> <span class="nt" style="color: navy;">-id2</span> Tuber <span class="nt" style="color: navy;">-seq2</span> GCF_000195955.2_ASM19595v2_genomic.fna</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FIXME! This test fails with the following error message:</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># > Segmentation fault</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># > Failed to ganerate statistics.</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></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;">echo</span> <span class="s2" style="color: #d14;">"RESULTS: OK</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: sim4db-unit-test</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"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Tests: atac-unit-test</span>
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2
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250#250298e80304390409b063185886417f177a00db"><strong>debian/tests/sim4db-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/sh -e</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"sim4db"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" 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="nv" style="color: teal;">$AUTOPKGTEST_TMP</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="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" 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: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test_data.tar.gz <span class="nb" style="color: #0086b3;">.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xzvf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run sim4db</span></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;">echo</span> <span class="s2" style="color: #d14;">"Testing sim4 for intra-species alignment...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">sim4db <span class="nt" style="color: navy;">-genomic</span> GCF_000195955.2_ASM19595v2_genomic.fna <span class="nt" style="color: navy;">-cdna</span> ESTs.fasta <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> <span class="nt" style="color: navy;">-output</span> results.sim4db</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> results.sim4db <span class="o" style="font-weight: 600;">]</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing sim4cc for inter-species alignment...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">sim4db <span class="nt" style="color: navy;">-genomic</span> GCF_000195855.1_ASM19585v1_genomic.fna <span class="nt" style="color: navy;">-cdna</span> ESTs.fasta <span class="se" style="color: #d14;">\</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"> <span class="nt" style="color: navy;">-interspecies</span> <span class="nt" style="color: navy;">-gff3</span> <span class="nt" style="color: navy;">-output</span> results.gff3</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> results.gff3 <span class="o" style="font-weight: 600;">]</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"RESULTS: OK</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span></pre>
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