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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>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmer/commit/5080553126487328686f72ec0ade5a83a47ec768">50805531</a></strong>
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<span>by Liubov Chuprikova</span>
<i>at 2018-06-15T12:06:31+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest to test atac for now
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<h4>5 changed files:</h4>
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<a href="#88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c">
debian/atac.docs
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
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debian/source/include-binaries
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<li class="file-stats">
<a href="#8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058">
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debian/tests/atac-unit-test
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debian/tests/control
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<a href="#9abb8ed09a0cbe2f2cce9c00629715155e9493b4">
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debian/tests/test-data/test_data.tar.gz
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<h4>Changes:</h4>
<li id="88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c">
<a href="https://salsa.debian.org/med-team/kmer/commit/5080553126487328686f72ec0ade5a83a47ec768#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></pre>
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<li id="d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<a href="https://salsa.debian.org/med-team/kmer/commit/5080553126487328686f72ec0ade5a83a47ec768#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/test-data/test_data.tar.gz</span></pre>
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<li id="8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058">
<a href="https://salsa.debian.org/med-team/kmer/commit/5080553126487328686f72ec0ade5a83a47ec768#8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058"><strong>debian/tests/atac-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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<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;">"atac"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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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">
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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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</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;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<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="shell"><span class="k" style="font-weight: 600;">fi</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="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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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<a href="https://salsa.debian.org/med-team/kmer/commit/5080553126487328686f72ec0ade5a83a47ec768#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: atac-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">Restrictions: allow-stderr</span></pre>
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