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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/a2979e81b138866d256554065a0f699c68b50a8f">a2979e81</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-19T17:09:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.12.1+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/e03d335572eee45576ca9689f32106cf290edae0">e03d3355</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-19T17:09:13+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.12.1+ds'
Update to upstream version '2.12.1+ds'
with Debian dir a9391d5a5282d2937c7ed2f1758f4ceec356c9a8</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/94003298665bfce4d8d0c820279f8240baaacc85">94003298</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-06-19T18:01:02+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
</a>
</li>
<li class="file-stats">
<a href="#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
ariba/ref_genes_getter.py
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/ariba/compare/5d1142d924d972f1f5de5ea5dca0f69ef3d75e99...94003298665bfce4d8d0c820279f8240baaacc85#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:17.<span class="idiff left right">04</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="docker"><span class="k" style="font-weight: 600;">FROM</span><span class="s" style="color: #d14;"> ubuntu:17.<span class="idiff left right">10</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: navy;">--no-install-recommends</span> <span class="nt" style="color: navy;">-y</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,7 +29,7 @@ ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="a</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>git clone https://github.com/sanger-pathogens/ariba.git <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>ariba <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> git checkout v2.1<span class="idiff left right">0.1</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> git checkout v2.1<span class="idiff left right">2.0</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> python3 setup.py <span class="nb" style="color: #0086b3;">test</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> python3 setup.py <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="docker"></span>
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<li id="acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
<a href="https://salsa.debian.org/med-team/ariba/compare/5d1142d924d972f1f5de5ea5dca0f69ef3d75e99...94003298665bfce4d8d0c820279f8240baaacc85#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4"><strong>ariba/ref_genes_getter.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="190" 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">@@ -190,7 +190,7 @@ class RefGenesGetter:</td>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python"></span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="nd">@classmethod</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">db_name</span><span class="p">,</span> <span class="n" style="color: #333;">outdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="s" style="color: #d14;">'plasmidfinder'</span><span class="p">,</span> <span class="s" style="color: #d14;">'resfinder'</span><span class="p">,</span> <span class="s" style="color: #d14;">'virulence<span class="idiff left right">_</span>finder'</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">db_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">{</span><span class="s" style="color: #d14;">'plasmidfinder'</span><span class="p">,</span> <span class="s" style="color: #d14;">'resfinder'</span><span class="p">,</span> <span class="s" style="color: #d14;">'virulencefinder'</span><span class="p">}</span></span>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'git clone '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'https://bitbucket.org/genomicepidemiology/'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">db_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_db.git '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">outdir</span></span>
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" 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>
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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">@@ -497,13 +497,13 @@ class RefGenesGetter:</td>
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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498
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error mkdir/chdir '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">plasmid</span>finder.zip'</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">virulence</span>finder.zip'</span></span>
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501
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'curl -X POST --data "folder=virulencefinder&filename=virulencefinder.zip" -o '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' https://cge.cbs.dtu.dk/cge/download_data.php'</span></span>
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502
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Downloading data with:'</span><span class="p">,</span> <span class="n" style="color: #333;">cmd</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>
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503
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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504
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python"> <span class="n" style="color: #333;">common</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">syscall</span><span class="p">(</span><span class="s" style="color: #d14;">'unzip '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">zipfile</span><span class="p">)</span></span>
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505
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">plasmid</span>finder'</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">RefGenesGetter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_genetic_epi_database_from_bitbucket</span><span class="p">(</span><span class="s" style="color: #d14;">'<span class="idiff left right">virulence</span>finder'</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">git_commit</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">)</span></span>
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507
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chdir</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">)</span></span>
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508
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"></span>
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509
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509
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Combining downloaded fasta files...'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ariba (2.12.1+ds-1) UNRELEASED; 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"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Tue, 19 Jun 2018 17:09:34 +0200</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">ariba (2.12.0+ds-1) unstable; urgency=medium</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"> * New upstream release.</span>
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<a href="https://salsa.debian.org/med-team/ariba/compare/5d1142d924d972f1f5de5ea5dca0f69ef3d75e99...94003298665bfce4d8d0c820279f8240baaacc85#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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">@@ -55,7 +55,7 @@ vcfcall_mod = Extension(</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">minimap_mod</span><span class="p">,</span> <span class="n" style="color: #333;">fermilite_mod</span><span class="p">,</span> <span class="n" style="color: #333;">vcfcall_mod</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.12.<span class="idiff left right">0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.12.<span class="idiff left right">1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ARIBA: Antibiotic Resistance Identification By Assembly'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'test_run_data/*'</span><span class="p">]},</span></span>
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