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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/80c72a35e667185d3f9617b784cb5647da41afa0">80c72a35</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-11-08T10:44:26+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/javabuild: updated to correct path to the Butterfly source

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/e31909c50a7ceac07cf41889b3d8995647a399c9">e31909c5</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-11-08T11:42:36+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">forward more patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/f5e6572b569260cb9b8d953ba55bf26db76bbe6f">f5e6572b</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-11-08T11:42:37+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">combine some related patches

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/45515ca9019bb7722044c6f808c73deb642686e2">45515ca9</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2021-11-08T12:44:38+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 2.13.2+dfsg-2

</pre>

</li>

</ul>

<h4>17 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">

debian/clean

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

debian/copyright

</a>

</li>

<li class="file-stats">

<a href="#d08ceb79bc022f99d8f6551aff2c06694b04d5ca">

debian/javabuild

</a>

</li>

<li class="file-stats">

<a href="#fac0c62d9b907e6be145e02cf3d336278225d633">

debian/patches/fix-gcc-10.patch

</a>

</li>

<li class="file-stats">

<a href="#9c3921224f13bb64ee0668e34e9072c2d81fed1e">

debian/patches/fix_system_paths

</a>

</li>

<li class="file-stats">

<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">

debian/patches/hardening

</a>

</li>

<li class="file-stats">

<a href="#186931c89155f23d06c513c76cb8d6987b932b72">

<span class="deleted-file">

−

debian/patches/jellyfish-path

</span>

</a>

</li>

<li class="file-stats">

<a href="#5b7194c7e8e3451f085699bcc06c43a54154e5cc">

debian/patches/seqtk-trinity-hardening

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#c09a689737a512e48ae26e435a69f8ff8fb69286">

debian/patches/skip_blat

</a>

</li>

<li class="file-stats">

<a href="#51ab7c62e5764910368cd982395ef9307cfb98fc">

debian/patches/skip_gatk_test

</a>

</li>

<li class="file-stats">

<a href="#cdbdea031c43a7a081a4aa05bbaa408ec696faa3">

debian/patches/skip_tximportData_tests

</a>

</li>

<li class="file-stats">

<a href="#fb48b16f89b5d54f32262e7f7be24655af3ea0bd">

debian/patches/strip_m64

</a>

</li>

<li class="file-stats">

<a href="#dc57bc18aaf815e3e69b3ca9f2884f0d4c8f0926">

debian/patches/submake

</a>

</li>

<li class="file-stats">

<a href="#6043880397caaede2502d6dfb2b7278a569046b3">

debian/patches/update-paths

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.13.2+dfsg-2) unstable; urgency=medium</span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="plaintext"></span>

</pre>

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

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * debian/javabuild: updated to correct path to the Butterfly source</span>

</pre>

</td>

</tr>

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

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

</td>

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debian/copyright: Now that the Butterfly source is back in the</span>

</pre>

</td>

</tr>

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

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

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">    upstream tarball, adjust the paths accordingly here as well.</span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="6" 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">

6

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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="LC6" class="line" lang="plaintext">  * debian/patches: forwarded many patches upstream</span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="7" 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">

7

</td>

<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="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org>  Mon, 08 Nov 2021 12:44:15 +0100</span>

</pre>

</td>

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<td class="new_line diff-line-num new" 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"></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">trinityrnaseq (2.13.2+dfsg-1) unstable; urgency=medium</span>

</pre>

</td>

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

2

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

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

</pre>

</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f5f51601866c86e59a004bd93fa415f5675be8c5">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#f5f51601866c86e59a004bd93fa415f5675be8c5"><strong>debian/clean</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" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" 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="new_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">trinity-plugins/ParaFly/config.log</span>

</pre>

</td>

</tr>

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

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

2

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<td class="new_line diff-line-num" data-linenumber="2" 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">

2

</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">trinity-plugins/ParaFly/config.status</span></pre>

</td>

</tr>

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

3

</td>

<td class="new_line diff-line-num old" data-linenumber="3" 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="LC3" class="line" lang="plaintext">Butterfly/src/sample_data/c1.graph.allProbPaths.fasta</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,8 +34,7 @@ Files: debian/*</td>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">Copyright: (c) 2015 Michigan State University</span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">License: BSD-3-clause</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">#Files: Butterfly/src/src/NWalign.java</span>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">Files: debian/patches/butterfly</span>

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<td class="old_line diff-line-num new" 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="LC37" class="line" lang="plaintext">Files: Butterfly/Butterfly/src/src/NWalign.java</span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">Copyright: Ahmed Moustafa <ahmed@users.sf.net></span>

</pre>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">License: GPL-2+</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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</li>

<li id="d08ceb79bc022f99d8f6551aff2c06694b04d5ca">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#d08ceb79bc022f99d8f6551aff2c06694b04d5ca"><strong>debian/javabuild</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Butterfly.jar Butterfly/src/src</span></pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Butterfly.jar <span class="idiff left right">Butterfly/</span>Butterfly/src/src</span></pre>

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<br>

</li>

<li id="fac0c62d9b907e6be145e02cf3d336278225d633">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#fac0c62d9b907e6be145e02cf3d336278225d633"><strong>debian/patches/fix-gcc-10.patch</strong></a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p"><span class="idiff left right">Description</span>: Fix gcc-10 build issue</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p"><span class="idiff left right">Subject</span>: Fix gcc-10 build issue</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/966876</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p"><span class="idiff left right">Author</span>: Andreas Tille <tille@debian.org></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p"><span class="idiff left right">From</span>: Andreas Tille <tille@debian.org></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Wed, 05 Aug 2020 12:44:59 +0200</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Forwarded: https://github.com/trinityrnaseq/bamsifter/commit/2fed73b5dd400ed8ba38f3f63b385e0faff26045</span></span>

</pre>

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

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6

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<td class="new_line diff-line-num" 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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff">--- trinityrnaseq.orig/trinity-plugins/bamsifter/sift_bam_max_cov.cpp</span>

</pre>

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<td class="old_line diff-line-num" 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

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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;">+++ trinityrnaseq/trinity-plugins/bamsifter/sift_bam_max_cov.cpp</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c3921224f13bb64ee0668e34e9072c2d81fed1e">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#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="2463" 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="2463" 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">@@ -2463,6 +2463,15 @@ Forwarded: not-needed</td>

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2463

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<td class="new_line diff-line-num" data-linenumber="2463" 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="LC2463" class="line" lang="diff"> </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2464" 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">

2464

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<td class="new_line diff-line-num" data-linenumber="2464" 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="LC2464" class="line" lang="diff"> my $usage = "\n\nusage: $0 reads.fa hash_size\n\n";</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2465" 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">

2465

</td>

<td class="new_line diff-line-num" data-linenumber="2465" 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">

2465

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

<pre style="margin: 0;"> <span id="LC2465" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2466" 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">

2466

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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="LC2466" class="line" lang="diff"><span class="p">@@ -11,7 +10,7 @@</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2467" 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">

2467

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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="LC2467" class="line" lang="diff"> my $hash_size = $ARGV[1] or die $usage;</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2468" 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">

2468

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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="LC2468" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2469" 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">

2469

</td>

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

<pre style="margin: 0;">+<span id="LC2469" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2470" 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">

2470

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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="LC2470" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2471" 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">

2471

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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="LC2471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $JELLYFISH_DIR = "/usr";</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2472" 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">

2472

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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="LC2472" class="line" lang="diff"> my $CPU = 4;</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2473" 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">

2473

</td>

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

<pre style="margin: 0;">+<span id="LC2473" class="line" lang="diff"> my $min_kmer_cov = 1;</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2466" 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="new_line diff-line-num new" data-linenumber="2474" 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">

2474

</td>

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

<pre style="margin: 0;">+<span id="LC2474" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num" data-linenumber="2466" 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">

2466

</td>

<td class="new_line diff-line-num" data-linenumber="2475" 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">

2475

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

<pre style="margin: 0;"> <span id="LC2475" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/util/misc/run_read_simulator_per_gene.pl</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2467" 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">

2467

</td>

<td class="new_line diff-line-num" data-linenumber="2476" 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">

2476

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<pre style="margin: 0;"> <span id="LC2476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/util/misc/run_read_simulator_per_gene.pl</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2468" 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">

2468

</td>

<td class="new_line diff-line-num" data-linenumber="2477" 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">

2477

</td>

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

<pre style="margin: 0;"> <span id="LC2477" class="line" lang="diff"><span class="p">@@ -5,8 +5,6 @@</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="d6c09299b1f914372840e8fd6fcc850f8a11b236">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</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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1

</td>

<td class="new_line diff-line-num" 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="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>

</pre>

</td>

</tr>

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

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

2

</td>

<td class="new_line diff-line-num" data-linenumber="2" 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">

2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: add standard CXXFLAGS CPPFLAGS to Chrysalis & scaffold_iworm_contigs</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/trinityrnaseq/Chrysalis/pull/1</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">and https://github.com/trinityrnaseq/trinityrnaseq/pull/1090</span></span>

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3

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Chrysalis/Makefile</span></span>

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4

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Chrysalis/Makefile</span></span>

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5

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -1,10 +1,10 @@</span></span>

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</li>

<li id="186931c89155f23d06c513c76cb8d6987b932b72">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#186931c89155f23d06c513c76cb8d6987b932b72"><strong>debian/patches/jellyfish-path</strong>

deleted

</a>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description:Jellyfish path</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/util/misc/run_jellyfish.pl</span></span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/util/misc/run_jellyfish.pl</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">@@ -11,7 +11,7 @@</span></span>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"> my $hash_size = $ARGV[1] or die $usage;</span>

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> </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;">-my $JELLYFISH_DIR = $FindBin::RealBin . "/../../trinity-plugins/jellyfish-1.1.3";</span></span>

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9

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+my $JELLYFISH_DIR = "/usr";</span></span>

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10

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> my $CPU = 4;</span>

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11

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> my $min_kmer_cov = 1;</span>

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

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<br>

</li>

<li id="5b7194c7e8e3451f085699bcc06c43a54154e5cc">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#5b7194c7e8e3451f085699bcc06c43a54154e5cc"><strong>debian/patches/seqtk-trinity-hardening</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 <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Subject: Add LDFALGS CPPFLAGS and unshadw CFALGS<span class="idiff left right"> for seqtk-trinity-0.0.2</span></span></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Add LDFALGS CPPFLAGS and unshad<span class="idiff left right">o</span>w CFALGS</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/trinityrnaseq/seqtk-trinity/pull/1/files</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/trinity-plugins/seqtk-trinity/Makefile</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/trinity-plugins/seqtk-trinity/Makefile</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -1,10 +1,10 @@</span></span>

</pre>

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<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">which_command_v</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">jellyfish-path</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">update-paths</span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">collections15-to-4</span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">0002-fix_istream_failure_call.patch</span>

</pre>

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</li>

<li id="c09a689737a512e48ae26e435a69f8ff8fb69286">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#c09a689737a512e48ae26e435a69f8ff8fb69286"><strong>debian/patches/skip_blat</strong></a>

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

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>

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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 blat</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

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<pre style="margin: 0;"> <span id="LC4" 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="LC5" 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="LC6" class="line" lang="diff"><span class="p">@@ -11,7 +11,6 @@</span></span>

</pre>

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</li>

<li id="51ab7c62e5764910368cd982395ef9307cfb98fc">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#51ab7c62e5764910368cd982395ef9307cfb98fc"><strong>debian/patches/skip_gatk_test</strong></a>

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1

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

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></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>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" 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="LC5" 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="LC6" class="line" lang="diff"><span class="p">@@ -8,7 +8,6 @@</span></span>

</pre>

</td>

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<br>

</li>

<li id="cdbdea031c43a7a081a4aa05bbaa408ec696faa3">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#cdbdea031c43a7a081a4aa05bbaa408ec696faa3"><strong>debian/patches/skip_tximportData_tests</strong></a>

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1

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

</pre>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></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="p">Forwarded: not-needed</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" 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="LC5" 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="LC6" class="line" lang="diff"><span class="p">@@ -8,7 +8,6 @@</span></span>

</pre>

</td>

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<br>

</li>

<li id="fb48b16f89b5d54f32262e7f7be24655af3ea0bd">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#fb48b16f89b5d54f32262e7f7be24655af3ea0bd"><strong>debian/patches/strip_m64</strong></a>

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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 <crusoe@debian.org></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Subject: remove -m64 flag, hopefully helps arm64 compile</span></span>

</pre>

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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="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Chrysalis/CMakeLists.txt</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Chrysalis/CMakeLists.txt</span></span>

</pre>

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5

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="p">@@ -13,7 +13,7 @@</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="dc57bc18aaf815e3e69b3ca9f2884f0d4c8f0926">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#dc57bc18aaf815e3e69b3ca9f2884f0d4c8f0926"><strong>debian/patches/submake</strong></a>

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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 <<span class="idiff left right">michael.crusoe@gmail.com</span>></span></span>

</pre>

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

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<td class="new_line diff-line-num new" 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">From: Michael R. Crusoe <<span class="idiff left right">crusoe@debian.org</span>></span></span>

</pre>

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2

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<td class="new_line diff-line-num" data-linenumber="2" 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">

2

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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>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/trinityrnaseq/Inchworm/pull/1</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="p">and https://github.com/trinityrnaseq/trinity_ext_sample_data/pull/2</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">and https://github.com/trinityrnaseq/trinityrnaseq/pull/1091</span></span>

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3

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6

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- trinityrnaseq.orig/Inchworm/Makefile</span></span>

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4

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ trinityrnaseq/Inchworm/Makefile</span></span>

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5

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"><span class="p">@@ -1,8 +1,8 @@</span></span>

</pre>

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<br>

</li>

<li id="6043880397caaede2502d6dfb2b7278a569046b3">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#6043880397caaede2502d6dfb2b7278a569046b3"><strong>debian/patches/update-paths</strong></a>

<hr>

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1

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<td class="new_line diff-line-num" 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="diff"><span class="p">Description: Updates the main Trinity program to use FHS paths</span></span>

</pre>

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2

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<td class="new_line diff-line-num old" data-linenumber="2" 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="LC2" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <<span class="idiff left">m</span>crusoe@<span class="idiff right">msu.edu</span>></span></span>

</pre>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@<span class="idiff left right">debian.org</span>></span></span>

</pre>

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

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<td class="new_line diff-line-num new" 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="p">Forwarded: no<span class="idiff left right">t-needed</span></span></span>

</pre>

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4

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<td class="new_line diff-line-num" data-linenumber="4" 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">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Updated: 2015-02-22</span></span>

</pre>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>

</pre>

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6

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<td class="new_line diff-line-num" 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

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- trinityrnaseq.orig/Trinity</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/5179a51e66583ac0501467f2cc53a489c7d98e57...45515ca9019bb7722044c6f808c73deb642686e2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,7 @@ override_dh_auto_clean:</td>

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46

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<td class="new_line diff-line-num" 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">

46

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">override_dh_auto_test:</span>

</pre>

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<td class="old_line diff-line-num" 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">

47

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<td class="new_line diff-line-num" 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">

47

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>

</pre>

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48

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48

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">     java -cp Butterfly.jar TransAssembly_allProbPaths -N 10000 -L 300 \</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="49" 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">

49

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<td class="new_line diff-line-num old" data-linenumber="49" 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="LC49" class="line" lang="plaintext">             -F 300 -C Butterfly/src/sample_data/c1.graph --stderr -V 20</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="50" 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="new_line diff-line-num new" data-linenumber="49" 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">

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">             -F 300 -C <span class="idiff left right">Butterfly/</span>Butterfly/src/sample_data/c1.graph --stderr -V 20</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="50" 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">

50

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<td class="new_line diff-line-num" data-linenumber="50" 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">

50

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">endif</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="51" 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">

51

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<td class="new_line diff-line-num" data-linenumber="51" 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">

51

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="52" 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">

52

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52

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

</pre>

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