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<h3>
Sascha Steinbiss pushed to branch upstream
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/47a544832c5305ba60a217e0160cf63717507bf0">47a54483</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-03-05T00:27:53+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.11.1+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/313bcec670249a186151e8a7ab3e859194149505">313bcec6</a></strong>
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<span>by Sascha Steinbiss</span>
<i>at 2018-03-05T09:09:54+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'upstream' of salsa.debian.org:med-team/ariba into upstream
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
ariba/ref_genes_getter.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/ariba/compare/110e4fec224bf2b28e3ca5380bb677e0295e757b...313bcec670249a186151e8a7ab3e859194149505#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</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">@@ -8,9 +8,9 @@ addons:</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">libgfortran3</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">libncurses5-dev</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"><span class="na" style="color: teal;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="idiff left"> </span><span class="pi"><span class="idiff">-</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="s" style="color: #d14;"><span class="idiff right">3.4"</span></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="pi"><span class="idiff left">-</span></span><span class="idiff"> </span><span class="s1" style="color: #d14;"><span class="idiff">'</span></span><span class="s" style="color: #d14;"><span class="idiff right">3.4'</span></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"><span class="na" style="color: teal;">sudo</span><span class="pi">:</span> <span class="no" style="color: teal;">false</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"><span class="na" style="color: teal;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"><span class="idiff left"> </span><span class="pi"><span class="idiff">-</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="s" style="color: #d14;"><span class="idiff">source</span></span><span class="nv" style="color: teal;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">./install_dependencies.sh"</span></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"><span class="pi"><span class="idiff left">-</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">source ./install_dependencies.sh</span></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="idiff left"> </span><span class="pi"><span class="idiff">-</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="s" style="color: #d14;"><span class="idiff">python</span></span><span class="nv" style="color: teal;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">setup.py</span></span><span class="nv" style="color: teal;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">test"</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"><span class="pi"><span class="idiff left">-</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">python setup.py test</span></span></span></pre>
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<li id="acaa9a3bc0fc8ad5b28b290d79b7b26d3f71d6d4">
<a href="https://salsa.debian.org/med-team/ariba/compare/110e4fec224bf2b28e3ca5380bb677e0295e757b...313bcec670249a186151e8a7ab3e859194149505#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="41" 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="41" 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">@@ -41,7 +41,7 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_card_versions</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Getting available CARD versions'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" 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;">download_file</span><span class="p">(</span><span class="s" style="color: #d14;">'https://card.mcmaster.ca/download'</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_file</span><span class="p">,</span> <span class="n" style="color: #333;">max_attempts</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;">max_download_attempts</span><span class="p">,</span> <span class="n" style="color: #333;">sleep_time</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;">sleep_time</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.<span class="idiff left right">bz2</span>)"'''</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.<span class="idiff left right">(gz|bz2)</span>)"'''</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">versions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tmp_file</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></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">@@ -481,4 +481,3 @@ class RefGenesGetter:</td>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outprefix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="k" style="font-weight: 600;">exec</span><span class="p">(</span><span class="s" style="color: #d14;">'self._get_from_'</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;">ref_db</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'(outprefix)'</span><span class="p">)</span></span></pre>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"></span></pre>
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<a href="https://salsa.debian.org/med-team/ariba/compare/110e4fec224bf2b28e3ca5380bb677e0295e757b...313bcec670249a186151e8a7ab3e859194149505#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;">'2.11.<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;">'2.11.<span class="idiff left right">1</span>'</span><span class="p">,</span></span>
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59
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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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