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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/virulencefinder">Debian Med / virulencefinder</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/virulencefinder/commit/9c83e55a6e674a8ef97d0876325f851e14b3f4f4">9c83e55a</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-09-02T07:37:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0+git20190809.dde157a</pre>
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<strong><a href="https://salsa.debian.org/med-team/virulencefinder/commit/683e5a79e0887aee5a634722b7304e2d49322338">683e5a79</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-09-02T07:54:36Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.3+git20190809.dde157a</pre>
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<h4>2 changed files:</h4>
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<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<h4>Changes:</h4>
<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/virulencefinder/compare/79496ec401dacff79a9ae04bb70cea9dfc440224...683e5a79e0887aee5a634722b7304e2d49322338#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -17,7 +17,7 @@ RUN apt-get update -qq; \</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="docker"><span class="k" style="font-weight: 600;">ENV</span><span class="s" style="color: #d14;"> DEBIAN_FRONTEND Teletype</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="docker"></span>
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<td class="diff-line-num old_line" data-linenumber="19" 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="LC19" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Install python dependencies</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-U</span> biopython tabulate <span class="nv" style="color: #008080;">cgecore</span><span class="o" style="font-weight: 600;">==</span>1.4.2<span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>pip3 <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-U</span> <span class="nv" style="color: #008080;">biopython</span><span class="o" style="font-weight: 600;"><span class="idiff left">==</span></span><span class="idiff right">1.73</span> tabulate <span class="nv" style="color: #008080;">cgecore</span><span class="o" style="font-weight: 600;">==</span>1.4.2<span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Install kma</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>git clone <span class="nt" style="color: #000080;">--branch</span> 1.0.1 <span class="nt" style="color: #000080;">--depth</span> 1 https://bitbucket.org/genomicepidemiology/kma.git<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/virulencefinder/compare/79496ec401dacff79a9ae04bb70cea9dfc440224...683e5a79e0887aee5a634722b7304e2d49322338#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,7 +21,8 @@ isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and L</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">Setting up VirulenceFinder program</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">Setting up VirulenceFinder program </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Warning:**</span> Due to bugs in BioPython 1.74, if you are not using the Docker container, do not use that version if not using Python 3.7.</span>
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<td class="diff-line-num new_line" data-linenumber="26" 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="LC26" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Go to wanted location for virulencefinder</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd</span> /path/to/some/dir</span>
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