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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/metabit">Debian Med / metabit</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/ab3427bff60dd4e4f35451c1e973b32ff97838a5">ab3427bf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:39:21Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use git mode in watch file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/237d1f9539cb6cc2b9d3765ddbd7a015b6f6a344">237d1f95</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:40:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop get-orig-source, use +dfsg suffix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/fa3649ec75772aeb36fd218a1251c85e201d7de0">fa3649ec</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:41:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use markdown instead of python-markdown
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/776927135837119913e5cccf9256a1c2700b7dfb">77692713</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:43:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.0+git20170725.24cb3ee+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/a60267e07bd3dc76def7cd483719b7c3b1068b42">a60267e0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:43:49Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/fe61fbb3e16a3b50171ba072f25abefae532d196">fe61fbb3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:43:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.0+git20170725.24cb3ee+dfsg'
Update to upstream version '0.0+git20170725.24cb3ee+dfsg'
with Debian dir c7f197377f3a030faebc8c3f845d2bacd442866c</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/dedf24336b2e3c6f08d98f624025d8946a1ef68e">dedf2433</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:44:00Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper-compat 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/3488101753cbc20ae48f37558c7037348ac2193d">34881017</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:44:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/d3d983c60a28aa44692b8a8ba802c56e10d27fb8">d3d983c6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:44:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/0679ad05e3fcf15275038c83eb0dbd9dede7b7e9">0679ad05</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:44:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Secure URI in copyright format
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/40ab580d747796197b6a4b7aa4b8790fad076e3e">40ab580d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:44:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not parse d/changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/6b545856495f2496437ae5a7fa8aea3231c6a7e1">6b545856</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:46:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/metabit/commit/d0e6a0605500ee8853ebfe904599204f2fa34b69">d0e6a060</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-11T08:48:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Cleanup changelog from automatic changes
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
<span class="new-file">
+
.gitignore
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<span class="deleted-file">
−
debian/compat
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#fc932f0eaa389a4e2b93916f3995aae4019ea823">
<span class="deleted-file">
−
debian/get-orig-source
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#7a2912fbe6ceea94da65eb5e202db62fb52ac768">
metaBIT.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*.pyc</span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">metabit (0.0+<span class="idiff left right">20170220</span>-1) UNRELEASED; urgency=medium</span>
</pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">metabit (0.0+<span class="idiff left right">git20170725.24cb3ee+dfsg</span>-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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</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"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 25 Jul 2016 14:09:2</span>9 +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 11 Sep 2019 10:44:4</span>9 +0200</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">9</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" 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="3" 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">@@ -3,14 +3,14 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 9</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> python-all,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right">python-</span>markdown,</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> markdown,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> bowtie2</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">3.9.8</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/metabit.g</span>it</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/metabit.git</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: <span class="idiff left right">4.4.0</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/metab</span>it</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/metabit.git</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://bitbucket.org/Glouvel/metabit/wiki/</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Package: metabit</span>
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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 +21,7 @@ Depends: ${python:Depends},</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> r-base-core,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> metaphlan2,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> python-pysam,</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> libpicard-java<span class="idiff left right"> (>= 1.138+dfsg.1)</span>,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> libpicard-java,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> samtools,</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> radiant,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> bedtools,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" 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="43" 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">@@ -43,7 +43,7 @@ Description: analysing microbial profiles from high-throughput sequencing shotgu</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">Package: metabit-examples</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">Depends: ${misc:Depends}<span class="idiff left right">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Recommends: metabit</span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Description: example data for MetaBIT pipeline for high-throughput sequencing data</span>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"> MetaBIT is an integrative and automated metagenomic pipeline for</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: metaBIT</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: https://bitbucket.org/Glouvel/metabit/downloads</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Files-Excluded: */pypeline/yaml</span>
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<li id="fc932f0eaa389a4e2b93916f3995aae4019ea823">
<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#fc932f0eaa389a4e2b93916f3995aae4019ea823"><strong>debian/get-orig-source</strong>
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1
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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: #008080;">COMPRESS</span><span class="o" style="font-weight: 600;">=</span>xz</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Source/ { print $2 }'</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">MVERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ { print $2 }'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^\([0-9\.]\+\)[+~][-0-9]\+$/\1/'</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> ../tarballs</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../tarballs</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># need to clean up the tarballs dir first because upstream tarball might</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># contain a directory with unpredictable name</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell">git clone <span class="nt" style="color: #000080;">--quiet</span> https://bitbucket.org/Glouvel/metabit.git</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$NAME</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">MVERSION</span><span class="k" style="font-weight: 600;">}</span>+<span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">date</span> <span class="nt" style="color: #000080;">-d</span> @<span class="si" style="color: #d14;">$(</span>git show <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"%at"</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="si" style="color: #d14;">)</span> +%Y%m%d<span class="sb" style="color: #d14;">`</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># for esthetical reasons set file timestamps (if git-restore-mtime is installed)</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">git restore-mtime <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">true</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">TARDIR</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">VERSION</span><span class="k" style="font-weight: 600;">}</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NAME</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TARDIR</span><span class="k" style="font-weight: 600;">}</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TARDIR</span><span class="k" style="font-weight: 600;">}</span>/.git<span class="k" style="font-weight: 600;">*</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell">find <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TARDIR</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: #000080;">-path</span> <span class="k" style="font-weight: 600;">*</span>/pypeline/yaml | xargs <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nv" style="color: #008080;">GZIP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--best --no-name"</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: #000080;">--owner</span><span class="o" style="font-weight: 600;">=</span>root <span class="nt" style="color: #000080;">--group</span><span class="o" style="font-weight: 600;">=</span>root <span class="nt" style="color: #000080;">--mode</span><span class="o" style="font-weight: 600;">=</span>a+rX <span class="nt" style="color: #000080;">-caf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span>_<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span>.orig.tar.<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">COMPRESS</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TARDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">TARDIR</span><span class="k" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -3,19 +3,19 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">RDIR := debian/$(DEB<span class="idiff left right">PKGNAM</span>E)/usr/lib/R/site-library/metabit</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><span class="idiff left right">include /usr/share/dpkg/default.mk</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">RDIR := debian/$(DEB<span class="idiff left right">_SOURC</span>E)/usr/lib/R/site-library/metabit</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">%:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@ --with python2</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh_auto_build</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> markdown<span class="idiff left right">_py -f README.html README.md</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> markdown<span class="idiff left right"> README.md > README.html</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> mkdir -p $(RDIR)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> for r in debian/$(DEB<span class="idiff left right">PKGNAM</span>E)/usr/share/metabit/nodes/tools/statax_Rmodule/*.R ; do \</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> for r in debian/$(DEB<span class="idiff left right">_SOURC</span>E)/usr/share/metabit/nodes/tools/statax_Rmodule/*.R ; do \</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> ln -s `echo $$r | sed 's:.*/usr:../../../..:'` $(RDIR) ; \</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> done</span></pre>
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<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># version=3</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># upstream has not proper versioning</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</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">opts="mode=git,pretty=0.0+git%cd.%h,repacksuffix=+dfsg,dversionmangle=auto,repack,compression=xz" \</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://bitbucket.org/Glouvel/metabit.git HEAD</span></pre>
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<a href="https://salsa.debian.org/med-team/metabit/compare/66d5c039b62c068172cf94499da78e12a03916a3...d0e6a0605500ee8853ebfe904599204f2fa34b69#7a2912fbe6ceea94da65eb5e202db62fb52ac768"><strong>metaBIT.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">@@ -36,7 +36,8 @@ _tools = {"filterMetaphlan": ["nodes", "tools", "filterMetaphlan.py"],</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">"doPcoa"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"statax_Rmodule"</span><span class="p">,</span> <span class="s" style="color: #d14;">"doPcoa.R"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">"doClust"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"statax_Rmodule"</span><span class="p">,</span> <span class="s" style="color: #d14;">"doClust.R"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"doDiv"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"statax_Rmodule"</span><span class="p">,</span> <span class="s" style="color: #d14;">"doDiv.R"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"doHeatmap"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"statax_Rmodule"</span><span class="p">,</span> <span class="s" style="color: #d14;">"doHeatmap.R"</span><span class="p">]}</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"doHeatmap"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"statax_Rmodule"</span><span class="p">,</span> <span class="s" style="color: #d14;">"doHeatmap.R"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">"doBarplot"</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">"nodes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"statax_Rmodule"</span><span class="p">,</span> <span class="s" style="color: #d14;">"doBarplot.R"</span><span class="p">]}</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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43
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<pre style="margin: 0;"> <span id="LC43" 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="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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