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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/snp-sites">Debian Med / snp-sites</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/snp-sites/commit/8f060bf0c1aa1b491f447c6b707bf57dc81796e3">8f060bf0</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2018-10-06T15:54:42Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.1</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#cd089ae45ce870c45e434019e8f1ed4f066cd425">
<span class="new-file">
+
_config.yml
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/8f060bf0c1aa1b491f447c6b707bf57dc81796e3#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,3 +33,6 @@ run-all-tests*</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">src/snp-sites</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">tests/.deps/*</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">tests/.dirstamp</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"># vagrant runtime stuff</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.vagrant</span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="plaintext">ubuntu-*-cloudimg-console.log</span></pre>
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<li id="6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/8f060bf0c1aa1b491f447c6b707bf57dc81796e3#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,7 +6,7 @@ FROM debian:testing</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#</span></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="7" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Authorship</span></span>
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<td class="diff-line-num old_line" data-linenumber="8" 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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<td class="diff-line-num new_line" data-linenumber="8" 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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="docker"><span class="k" style="font-weight: 600;">MAINTAINER</span><span class="s" style="color: #d14;"> <span class="idiff left right">ap13</span>@sanger.ac.uk</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="docker"><span class="k" style="font-weight: 600;">MAINTAINER</span><span class="s" style="color: #d14;"> <span class="idiff left right">path-help</span>@sanger.ac.uk</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="docker"></span>
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<td class="diff-line-num old_line" data-linenumber="11" 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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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" 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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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Pull in packages from testing</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,6 +14,6 @@ MAINTAINER ap13@sanger.ac.uk</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get update <span class="nt" style="color: navy;">-qq</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="LC15" class="line" lang="docker"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Install <span class="idiff left right">Roary</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="18" 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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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Install <span class="idiff left right">SNP-sites</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="18" 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="LC18" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nb" style="color: #0086b3;">install </span>snp-sites</span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span>apt-get <span class="nt" style="color: navy;"><span class="idiff left">-y</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">install </span>snp-sites</span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/8f060bf0c1aa1b491f447c6b707bf57dc81796e3#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># SNP-sites</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">Rapidly extracts SNPs from a multi-FASTA alignment.</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/snp-sites.png?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/snp-sites)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE)</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000056-brightgreen.svg</span><span class="p">)</span>](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/snp-sites.png?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/snp-sites) </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE) </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000056-brightgreen.svg</span><span class="p">)</span>](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056) </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg</span><span class="p">)</span>](http://bioconda.github.io/recipes/gubbins/README.html) </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Container ready</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/container-ready-brightgreen.svg</span><span class="p">)</span>](https://quay.io/repository/biocontainers/gubbins) </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Docker Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/build/sangerpathogens/gubbins.svg</span><span class="p">)</span>](https://hub.docker.com/r/sangerpathogens/gubbins) </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Docker Pulls</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/pulls/sangerpathogens/gubbins.svg</span><span class="p">)</span>](https://hub.docker.com/r/sangerpathogens/gubbins) </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#introduction</span><span class="p">)</span></span>
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<li id="b33892fbddeffc3368077b4904ad0b3d562a7312">
<a href="https://salsa.debian.org/med-team/snp-sites/commit/8f060bf0c1aa1b491f447c6b707bf57dc81796e3#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.4.<span class="idiff left right">0</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.4.<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/snp-sites/commit/8f060bf0c1aa1b491f447c6b707bf57dc81796e3#cd089ae45ce870c45e434019e8f1ed4f066cd425"><strong>_config.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: teal;">theme</span><span class="pi">:</span> <span class="s" style="color: #d14;">jekyll-theme-cayman</span></span></pre>
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