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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

at <a href="https://salsa.debian.org/med-team/trinityrnaseq">Debian Med / trinityrnaseq</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/1e726c88a402e59cfa28b7959559d7c47c51d0b2">1e726c88</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T08:27:06+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">r-cran-argparse

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/613e03945f42ab3e5ddd790939f0d4269f07191b">613e0394</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T10:29:02+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">r-cran-goplot is also needed

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/3eaa7162fac46e6db0275bfdc4f221744996aeba">3eaa7162</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T10:48:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/cb8682cca32ea815b305a7328ee0ad33fd2e4bf5">cb8682cc</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T11:07:27+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/f3c8024affba8a82fdb3fd97ca6b6e453e0e22c4">f3c8024a</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T12:06:59+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">r-bioc-dexseq too

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/431bf5ea27a8891d2f21e128d87ac81e13c3c3ab">431bf5ea</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T12:40:25+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">python3-hisat2 needed for hisat2_extract_splice_sites.py

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/eefd189599c02f10388c9546e5c150d7ed863e9a">eefd1895</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T13:10:36+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install PyLib/Pipeliner.py

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/887187f6ed9e008ead04cc8c0e3d5b22f578fe47">887187f6</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T13:37:51+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Set PICARD_HOME default of /usr/share/java

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/d726fbcf23112e8509f586d728dce45f6b5be85c">d726fbcf</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T13:41:14+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip tests that require GATK4 until it gets packaged

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/7645c287103fc6a730cd9b0cd5df53ac06a021c0">7645c287</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T14:09:19+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">r-bioc-glimma

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/3d0dec2554de2fa180b694e463f754fde82981d6">3d0dec25</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T14:22:11+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip tests that require r-bioc-tximportdata

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/8c220e5b012601c2017980c0d9bd951b0211467b">8c220e5b</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T14:54:39+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">r-cran-readr

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/dbc1d9e31ae39d27fc54442988158d79d527ce1d">dbc1d9e3</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T14:55:59+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/submake: use $(MAKE) consistently

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/8aa33ac68af254439bba2b5dc024997e7aba42da">8aa33ac6</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T14:58:25+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add another LD_PRELOAD clear

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/dd9ca55fb2f54a535b451ca4f736760bb170ebaa">dd9ca55f</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-04-27T17:26:05+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Skip the remaining tests waiting for new packages

</pre>

</li>

</ul>

<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#9c3921224f13bb64ee0668e34e9072c2d81fed1e">

debian/patches/fix_system_paths

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#c09a689737a512e48ae26e435a69f8ff8fb69286">

<span class="new-file">

+

debian/patches/skip_blat

</span>

</a>

</li>

<li class="file-stats">

<a href="#51ab7c62e5764910368cd982395ef9307cfb98fc">

<span class="new-file">

+

debian/patches/skip_gatk_test

</span>

</a>

</li>

<li class="file-stats">

<a href="#94af5ac81c4aa36293c5d1cb777bba18e1c2a1ab">

<span class="new-file">

+

debian/patches/skip_r-bioc-dexseq

</span>

</a>

</li>

<li class="file-stats">

<a href="#2bcf4d68c971c9bcc6743448d4d08161d7b393a9">

<span class="new-file">

+

debian/patches/skip_r-cran-argpase

</span>

</a>

</li>

<li class="file-stats">

<a href="#cdbdea031c43a7a081a4aa05bbaa408ec696faa3">

<span class="new-file">

+

debian/patches/skip_tximportData_tests

</span>

</a>

</li>

<li class="file-stats">

<a href="#dc57bc18aaf815e3e69b3ca9f2884f0d4c8f0926">

<span class="new-file">

+

debian/patches/submake

</span>

</a>

</li>

<li class="file-stats">

<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">

debian/tests/control

</a>

</li>

<li class="file-stats">

<a href="#aab2726ed6daf419caf178b1480b6d7da8a85af6">

debian/tests/run-tests

</a>

</li>

<li class="file-stats">

<a href="#1c59a5b1423455bbaaab2ab4c6345c91350b4d44">

debian/trinityrnaseq.install

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,8 +5,9 @@ trinityrnaseq (2.10.0+dfsg-1) UNRELEASED; urgency=medium</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="5" 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">

5

</td>

<td class="diff-line-num new_line" data-linenumber="5" 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">

5

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * debhelper-compat 12</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num 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">

6

</td>

<td class="diff-line-num 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">

6

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * debian/control: Added</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_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">

7

</td>

<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">

7

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">      python3-htseq, rna-star, picard-tools, gmap, histat2, subread, kallisto,</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="8" 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">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="8" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">      r-bioc-{edger,deseq2,rots,ctc,biobase,qvalue,goseq,tximport},</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="8" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">      r-cran-{ape,fastcluster,gplots}, and liburi-perl deps</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="10" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      r-bioc-{edger,deseq2,rots,ctc,biobase,qvalue,goseq,tximport,dexseq,glimma},</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="10" 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">

</td>

<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">

9

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      r-cran-{ape,fastcluster,gplots,argparse,goplot,readr,tidyverse},</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="10" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">      liburi-perl deps, and python3-hisat2</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="10" 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">

10

</td>

<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">

11

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">  * Standards-Version: 4.5.0 (routine-update)</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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">

11

</td>

<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="plaintext">  * Refresh patches</span>

</pre>

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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">

12

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<td class="diff-line-num new_line" data-linenumber="13" 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">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">  * Add salsa-ci file (routine-update)</span>

</pre>

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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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,8 +15,15 @@ trinityrnaseq (2.10.0+dfsg-1) UNRELEASED; urgency=medium</td>

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<td class="diff-line-num 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">

14

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<td class="diff-line-num new_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="plaintext">  * Use secure URI in Homepage field.</span>

</pre>

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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">

15

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">  * debian/rules: seqtk-trinity now has a unversioned path</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" 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">

16

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">  * debian/patches/butterfly: restore missing Butterfly sources</span>

</pre>

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<td class="diff-line-num new old_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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<td class="diff-line-num new new_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">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">  * debian/patches/submake: use $(MAKE) consistently</span>

</pre>

</td>

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<td class="diff-line-num 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">

17

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<td class="diff-line-num new_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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">  * Install the new bamsfilter plugin</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC18" class="line" lang="plaintext">  * TODO: package r-bioc-{glimma,tximportData} and r-cran-{argparse,goplot}</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">  * Install trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">  * Install trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">  * Install PyLib/Pipeliner.py</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">  * Set PICARD_HOME default of /usr/share/java</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext">  * Skip tests that require GATK4 until it gets packaged</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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="25" 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="LC25" class="line" lang="plaintext">  * Skip tests that require r-bioc-tximportdata</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="19" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="26" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">  * Skip the remaining tests waiting for new packages </span>

</pre>

</td>

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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">

19

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<td class="diff-line-num new_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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="28" 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="LC28" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sun, 26 Apr 2020 17:01:55 +0200</span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>

</pre>

</td>

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<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="25" 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">@@ -25,6 +25,7 @@ Build-Depends: debhelper-compat (= 12),</td>

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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext">               r-cran-ape,</span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">               r-bioc-ctc,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" 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="LC27" class="line" lang="plaintext">               r-cran-gplots,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="28" 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="LC28" class="line" lang="plaintext">               r-cran-readr,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" 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="LC29" class="line" lang="plaintext">               r-bioc-biobase,</span>

</pre>

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">               r-bioc-qvalue,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="30" 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="LC31" class="line" lang="plaintext">               r-bioc-goseq,</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" 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="36" 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">@@ -35,7 +36,13 @@ Build-Depends: debhelper-compat (= 12),</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">               gmap,</span>

</pre>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">               hisat2,</span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">               subread,</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="39" 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="LC38" class="line" lang="plaintext">               kallisto</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="39" 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="LC39" class="line" lang="plaintext">               kallisto,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="LC40" class="line" lang="plaintext">               python3-hisat2</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="41" 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="LC41" class="line" lang="plaintext">#               r-cran-argparse,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="42" 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="LC42" class="line" lang="plaintext">#               r-cran-goplot,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="43" 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="LC43" class="line" lang="plaintext">#               r-bioc-dexseq,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="44" 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="LC44" class="line" lang="plaintext">#               r-bioc-glimma,</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" 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="45" 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="LC45" class="line" lang="plaintext">#               r-bioc-tximportdata</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" 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="46" 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="LC46" class="line" lang="plaintext">Standards-Version: 4.5.0</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" 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="47" 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="LC47" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/trinityrnaseq</span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/trinityrnaseq.git</span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="74" 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">@@ -67,6 +74,7 @@ Depends: ${shlibs:Depends},</td>

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67

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<td class="diff-line-num new_line" data-linenumber="74" 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">

74

</td>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">         python3-numpy,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="68" 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">

68

</td>

<td class="diff-line-num new_line" data-linenumber="75" 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">

75

</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">         ncbi-blast+,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="69" 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">

69

</td>

<td class="diff-line-num new_line" data-linenumber="76" 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">

76

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">         python3,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="70" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="77" 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">

77

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">         r-cran-readr,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="70" 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">

70

</td>

<td class="diff-line-num new_line" data-linenumber="78" 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">

78

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">         r-bioc-edger,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="71" 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">

71

</td>

<td class="diff-line-num new_line" data-linenumber="79" 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">

79

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">         r-bioc-deseq2,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="72" 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">

72

</td>

<td class="diff-line-num new_line" data-linenumber="80" 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">

80

</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">         r-bioc-rots,</span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="84" 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="92" 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">@@ -84,12 +92,18 @@ Depends: ${shlibs:Depends},</td>

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<td class="diff-line-num old_line" data-linenumber="84" 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">

84

</td>

<td class="diff-line-num new_line" data-linenumber="92" 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">

92

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext">         gmap,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="85" 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">

85

</td>

<td class="diff-line-num new_line" data-linenumber="93" 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">

93

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">         hisat2,</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="86" 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">

86

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<td class="diff-line-num new_line" data-linenumber="94" 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">

94

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">         subread,</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="87" 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">

87

</td>

<td class="diff-line-num new_line old" data-linenumber="95" 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">

</td>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">         kallisto</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="88" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="95" 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">

95

</td>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">         kallisto,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="88" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" 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">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">         python3-hisat2</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="88" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="97" 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">

97

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">#         r-cran-argparse,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="88" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">#         r-cran-goplot,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="88" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="99" 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">

99

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">#         r-bioc-dexseq,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="88" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="100" 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">

100

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">#         r-bioc-glimma</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="88" 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">

88

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<td class="diff-line-num new_line" data-linenumber="101" 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">

101

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="89" 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">

89

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<td class="diff-line-num new_line" data-linenumber="102" 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">

102

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext">            trinityrnaseq-examples,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="90" 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">

90

</td>

<td class="diff-line-num new_line old" data-linenumber="103" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">            tidyverse,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="91" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">            <span class="idiff left right">r-cran-</span>tidyverse,</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="91" 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">

91

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<td class="diff-line-num new_line" data-linenumber="104" 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">

104

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">            picard-tools</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="92" 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">

92

</td>

<td class="diff-line-num new_line old" data-linenumber="105" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">Suggests: collectl</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="93" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">Suggests: collectl,</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="93" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="106" 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">

106

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">          r-bioc-tximportdata</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="93" 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">

93

</td>

<td class="diff-line-num new_line" data-linenumber="107" 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">

107

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">Description: RNA-Seq De novo Assembly</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="94" 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">

94

</td>

<td class="diff-line-num new_line" data-linenumber="108" 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">

108

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"> Trinity represents a novel method for the efficient and robust de novo</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="95" 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">

95

</td>

<td class="diff-line-num new_line" data-linenumber="109" 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">

109

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"> reconstruction of transcriptomes from RNA-seq data. Trinity combines three</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c3921224f13bb64ee0668e34e9072c2d81fed1e">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#9c3921224f13bb64ee0668e34e9072c2d81fed1e"><strong>debian/patches/fix_system_paths</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2761" 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="2761" 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">@@ -2761,3 +2761,14 @@ Author: Tim Booth <tbooth@ceh.ac.uk></td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2761" 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">

2761

</td>

<td class="diff-line-num new_line" data-linenumber="2761" 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">

2761

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2761" class="line" lang="diff">     </span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2762" 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">

2762

</td>

<td class="diff-line-num new_line" data-linenumber="2762" 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">

2762

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2762" class="line" lang="diff">     print "$cmd\n";</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2763" 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">

2763

</td>

<td class="diff-line-num new_line" data-linenumber="2763" 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">

2763

</td>

<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2763" class="line" lang="diff"> }</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2764" 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">

2764

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2764" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2765" 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">

2765

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2765" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2766" 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">

2766

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2766" class="line" lang="diff"><span class="p">@@ -143,7 +143,7 @@</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2767" 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">

2767

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2767" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2768" 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">

2768

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2768" class="line" lang="diff">     args = parser.parse_args()</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2769" 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">

2769

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2769" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2770" 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">

2770

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2770" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    PICARD_HOME = os.getenv("PICARD_HOME")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2771" 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">

2771

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    PICARD_HOME = os.getenv("PICARD_HOME", "/usr/share/java")</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2772" 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">

2772

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2772" class="line" lang="diff">     if not PICARD_HOME:</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2773" 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">

2773

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2773" class="line" lang="diff">         exit("Error, missing path to Picard-Tools in $PICARD_HOME.")</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="2764" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="2774" 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">

2774

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<pre style="margin: 0;">+<span id="LC2774" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,3 +12,9 @@ python3</td>

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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">

12

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12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">unfix_num_of_cores</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="13" 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">

13

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13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">hardening</span>

</pre>

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<td class="diff-line-num 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">

14

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<td class="diff-line-num 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">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">seqtk-trinity-hardening</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" 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="15" 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">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">skip_gatk_test</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" 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="16" 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">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">skip_tximportData_tests</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" 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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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">submake</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" 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="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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">skip_r-cran-argpase</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" 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="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">skip_r-bioc-dexseq</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="15" 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="20" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">skip_blat</span></pre>

</td>

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<br>

</li>

<li id="c09a689737a512e48ae26e435a69f8ff8fb69286">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#c09a689737a512e48ae26e435a69f8ff8fb69286"><strong>debian/patches/skip_blat</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: skip tests with a dependency on blat</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="3" 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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="4" 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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="5" 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">

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -9,8 +9,7 @@</span></span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> test_PtR \</span>

</pre>

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7

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test_SuperTranscript \</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="8" 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">

8

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> test_TPM_weighted_gene_length \</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_ExN50 \</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_Assembly_DiffReadFormattings</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test_ExN50</span></span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> test:</span></pre>

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<br>

</li>

<li id="51ab7c62e5764910368cd982395ef9307cfb98fc">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#51ab7c62e5764910368cd982395ef9307cfb98fc"><strong>debian/patches/skip_gatk_test</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Skip tests that require GATK4 until it gets packaged</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -8,7 +8,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> test_profiling_report \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test_PtR \</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> test_DTU \</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_VariantCalling \</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> test_tximport \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> test_SuperTranscript \</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> test_GOplot \</span></pre>

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<br>

</li>

<li id="94af5ac81c4aa36293c5d1cb777bba18e1c2a1ab">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#94af5ac81c4aa36293c5d1cb777bba18e1c2a1ab"><strong>debian/patches/skip_r-bioc-dexseq</strong></a>

<hr>

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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: skip tests with a dependency on r-bioc-dexseq</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -7,7 +7,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> test_GOSeq_trinotate_pipe \</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test_profiling_report \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> test_PtR \</span>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_DTU \</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> test_SuperTranscript \</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> test_TPM_weighted_gene_length \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> test_ExN50 \</span></pre>

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<br>

</li>

<li id="2bcf4d68c971c9bcc6743448d4d08161d7b393a9">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#2bcf4d68c971c9bcc6743448d4d08161d7b393a9"><strong>debian/patches/skip_r-cran-argpase</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: skip tests with a dependency on r-cran-argparse</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_GOSeq_trinotate_pipe/Makefile</span></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-DIRS = Spombe_runGOseqOnly test_GOplot Spombe_analyzeDiffExprWithGOseq</span></span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+DIRS = Spombe_runGOseqOnly Spombe_analyzeDiffExprWithGOseq</span></span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> test:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -9,7 +9,6 @@</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> test_PtR \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> test_DTU \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> test_SuperTranscript \</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_GOplot \</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> test_TPM_weighted_gene_length \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> test_ExN50 \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> test_Assembly_DiffReadFormattings</span></pre>

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<br>

</li>

<li id="cdbdea031c43a7a081a4aa05bbaa408ec696faa3">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#cdbdea031c43a7a081a4aa05bbaa408ec696faa3"><strong>debian/patches/skip_tximportData_tests</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: r-bioc-tximportdata is 400MiB+ package</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -8,7 +8,6 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> test_profiling_report \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test_PtR \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> test_DTU \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-test_tximport \</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> test_SuperTranscript \</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> test_GOplot \</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> test_TPM_weighted_gene_length \</span></pre>

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<br>

</li>

<li id="dc57bc18aaf815e3e69b3ca9f2884f0d4c8f0926">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#dc57bc18aaf815e3e69b3ca9f2884f0d4c8f0926"><strong>debian/patches/submake</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Enable better use of sub-make</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Inchworm/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Inchworm/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> all:</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">   mkdir -p build</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && $(MAKE) DESTDIR=../ install</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> clean:</span>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff">  @echo cleaning</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (cd build && make clean) || :</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (cd build && $(MAKE) clean) || :</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff">  rm -rf ./build ./bin</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -57,19 +57,19 @@</span></span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> test_trinity:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd sample_data/test_Trinity_Assembly && make test</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd sample_data/test_Trinity_Assembly && $(MAKE) test</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> # note 'test_all': ** this is for a more advanced installation including devel features **</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> test_all:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd sample_data/ && make test_all</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd sample_data/ && $(MAKE) test_all</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff">  ./__pull_trinity_ext_sample_data.sh</span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd trinity_ext_sample_data/ && make test</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd trinity_ext_sample_data/ && $(MAKE) test</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> test_clean:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd sample_data/ && make clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd trinity_ext_sample_data/ && make clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd sample_data/ && $(MAKE) clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd trinity_ext_sample_data/ && $(MAKE) clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> ###################################################################</span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/sample_data/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/sample_data/Makefile</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -3,7 +3,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> test_all: test_trin_assembly</span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> test_trin_assembly:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd test_Trinity_Assembly && make test_all</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd test_Trinity_Assembly && $(MAKE) test_all</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> clean:</span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity-plugins/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity-plugins/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -26,11 +26,11 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> htslib.ok:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd htslib && autoreconf && ./configure --prefix=`pwd` && make && make install</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd htslib && autoreconf && ./configure --prefix=`pwd` && $(MAKE) && $(MAKE) install</span></span>

</pre>

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62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff">  @touch htslib.ok</span>

</pre>

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63

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="64" 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">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> bamsifter_target: htslib.ok</span>

</pre>

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65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd bamsifter && make && cp bamsifter ../BIN/</span></span>

</pre>

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66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd bamsifter && $(MAKE) && cp bamsifter ../BIN/</span></span>

</pre>

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67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>

</pre>

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68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> ##################################</span>

</pre>

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69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> ### Needed for downstream analyses</span>

</pre>

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70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -53,8 +53,8 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff">  rm -f ./Trimmomatic # rm symlink</span>

</pre>

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72

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff">  cd slclust && $(MAKE) clean</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff">  cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd htslib && make clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd bamsifter && make clean</span></span>

</pre>

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76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd htslib && $(MAKE) clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd bamsifter && $(MAKE) clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff">  rm -f ./htslib.ok</span>

</pre>

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79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">  @echo "\n\n** Done cleaning plugins area **"</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_SuperTranscript/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_SuperTranscript/Makefile</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> test:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff">  ./runMe.sh</span>

</pre>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd indiv_tests && make test</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd indiv_tests && $(MAKE) test</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="88" 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="LC88" class="line" lang="diff">  @touch test</span>

</pre>

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> clean:</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" class="line" lang="diff">  ./cleanMe.sh</span>

</pre>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- cd indiv_tests && make clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cd indiv_tests && $(MAKE) clean</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="97" 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="LC97" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/drosoph_denovo.samples.txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/drosoph_denovo.samples.txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="103" 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">

103

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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="104" 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">

104

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="105" 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">

105

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="106" 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">

106

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="107" 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">

107

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="108" 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">

108

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="109" 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">

109

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="110" 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">

110

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/mouse_denovo.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="111" 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">

111

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="112" 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">

112

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/mouse_denovo.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="113" 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">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="114" 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">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="115" 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">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="116" 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="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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">

</td>

<td class="diff-line-num new new_line" data-linenumber="117" 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">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="118" 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="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="119" 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">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="120" 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="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="121" 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="LC121" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/schizo_denovo.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="124" 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="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=misc_tests/schizo_denovo.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="125" 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="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="126" 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="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="127" 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="LC127" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="128" 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="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="131" 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="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=drosoph.samples.txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="136" 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="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/10M/trinity_out_dir/Trinity.fasta SAMPLES=drosoph.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="137" 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="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" 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">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" 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">

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/DROSOPHILA/Annotations/Drosoph_coding.cdna SAMPLES=misc_tests/drosoph_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="143" 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">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="144" 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">

144

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="145" 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">

145

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="146" 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">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=mouse.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="147" 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">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="148" 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">

148

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/MOUSE_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel/trinity_out_dir/Trinity.fasta SAMPLES=mouse.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="149" 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">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="150" 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">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="151" 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">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="152" 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="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="153" 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">

153

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

</td>

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<td class="diff-line-num new new_line" data-linenumber="154" 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="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/regev_genome_portal/RESOURCES/mouse/mm9/Annotations/mm9_ucsc_genomeStudio_genes/mm9_ucsc_genomeStudio_genes.gtf.trans.fa SAMPLES=misc_tests/mouse_ref.samples.txt</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="155" 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">

155

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="157" 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="LC157" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="0" 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="158" 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="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=schizo.samples.txt</span></span>

</pre>

</td>

</tr>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/seq/RNASEQ/TRINITY_DEVEL_DATA/SCHIZO_RNASEQ_METHODS_ANALYSIS/10M/SS_trin_test/run_devel_trinity/trinity_out_dir/Trinity.fasta SAMPLES=schizo.samples.txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="p">@@ -1 +1,2 @@</span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-make TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+MAKE=${MAKE:-make}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+${MAKE} TRINITY_FASTA=/home/unix/bhaas/utilities/schizo/SP2_GeneDB.290110.prot_coding.cds.nr SAMPLES=misc_tests/schizo_ref.samples.txt</span></span></pre>

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<br>

</li>

<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>

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<td class="diff-line-num old_line" data-linenumber="1" 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">

1

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<td class="diff-line-num new_line" data-linenumber="1" 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">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-tests</span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @, @builddeps@</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" 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="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, @builddeps@<span class="idiff left right">, r-cran-tidyverse</span></span>

</pre>

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3

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<td class="diff-line-num 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">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>

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</li>

<li id="aab2726ed6daf419caf178b1480b6d7da8a85af6">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#aab2726ed6daf419caf178b1480b6d7da8a85af6"><strong>debian/tests/run-tests</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,6 +15,6 @@ rm -f trinityrnaseq/sample_data</td>

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<td class="diff-line-num new_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">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-rs</span> /usr/share/trinityrnaseq/sample_data trinityrnaseq/</span>

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16

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<td class="diff-line-num new_line" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-rs</span> /usr/share/trinityrnaseq/trinity_ext_sample_data trinityrnaseq/</span>

</pre>

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17

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd </span>trinityrnaseq/sample_data</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" 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">

18

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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC18" class="line" lang="shell">make test_all</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="19" 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="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">

18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nv" style="color: #008080;"><span class="idiff left">LD_PRELOAD</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span>make test_all</span>

</pre>

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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">

19

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<td class="diff-line-num new_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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../trinity_ext_sample_data</span>

</pre>

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20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nv" style="color: #008080;">LD_PRELOAD</span><span class="o" style="font-weight: 600;">=</span> make <span class="nb" style="color: #0086b3;">test</span></span></pre>

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</li>

<li id="1c59a5b1423455bbaaab2ab4c6345c91350b4d44">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/550d8458ef63ffaeb289c1e494e99962051a1ea9...dd9ca55fb2f54a535b451ca4f736760bb170ebaa#1c59a5b1423455bbaaab2ab4c6345c91350b4d44"><strong>debian/trinityrnaseq.install</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" 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="9" 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">@@ -9,3 +9,6 @@ Trinity /usr/lib/trinityrnaseq</td>

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<td class="diff-line-num old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line" data-linenumber="9" 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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="php"><span class="nx">PerlLib</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinityrnaseq</span><span class="o" style="font-weight: 600;">/</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="10" 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">

10

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<td class="diff-line-num new_line" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="php"><span class="nx">util</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinityrnaseq</span><span class="o" style="font-weight: 600;">/</span></span>

</pre>

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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">

11

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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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="php"><span class="nx">trinity</span><span class="o" style="font-weight: 600;">-</span><span class="nx">plugins</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bamsifter</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bamsifter</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinityrnaseq</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinity</span><span class="o" style="font-weight: 600;">-</span><span class="nx">plugins</span><span class="o" style="font-weight: 600;">/</span><span class="nx">BIN</span><span class="o" style="font-weight: 600;">/</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="LC12" class="line" lang="php"><span class="nx">trinity</span><span class="o" style="font-weight: 600;">-</span><span class="nx">plugins</span><span class="o" style="font-weight: 600;">/</span><span class="nx">COLLECTL</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examine_resource_usage_profiling</span><span class="o" style="font-weight: 600;">.</span><span class="nx">pl</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinityrnaseq</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinity</span><span class="o" style="font-weight: 600;">-</span><span class="nx">plugins</span><span class="o" style="font-weight: 600;">/</span><span class="nx">COLLECTL</span><span class="o" style="font-weight: 600;">/</span></span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="php"><span class="nx">trinity</span><span class="o" style="font-weight: 600;">-</span><span class="nx">plugins</span><span class="o" style="font-weight: 600;">/</span><span class="nx">DEXseq_util</span><span class="o" style="font-weight: 600;">/</span><span class="nx">dexseq_prepare_annotation</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinityrnaseq</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinity</span><span class="o" style="font-weight: 600;">-</span><span class="nx">plugins</span><span class="o" style="font-weight: 600;">/</span><span class="nx">DEXseq_util</span><span class="o" style="font-weight: 600;">/</span></span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="php"><span class="nx">PyLib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">Pipeliner</span><span class="o" style="font-weight: 600;">.</span><span class="nx">py</span> <span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">trinityrnaseq</span><span class="o" style="font-weight: 600;">/</span><span class="nx">PyLib</span><span class="o" style="font-weight: 600;">/</span></span></pre>

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