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<h3>
Alexandre Mestiashvili pushed to branch master
at <a href="https://salsa.debian.org/med-team/spades">Debian Med / spades</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/c9ac2dcb3f156e0fb7db065ac66730af8d427114">c9ac2dcb</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T09:37:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Create symlink to VERSION file in the place where spades is looking for it
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/3beaf1902ec9704cb2d2a475fde8bebaad839360">3beaf190</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T09:39:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update PYTHONPATH for spades wrapper
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/e2164b1512139fa481fe5ed4fc48bc1c168fdb72">e2164b15</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T13:19:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/rules, fix VERSION location for tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/c1d849a6f55e45a6aa9b02d7c85ca51678bb42a3">c1d849a6</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T13:33:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Inject PYTHONPATH for tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/55215be0fc15f22caeda63f554cb18bee2ea05d4">55215be0</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T13:34:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">qilt delete 0113_adjust_paths.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/c86d14166d3f49546ab7ad891c2e00a4e0e1e478">c86d1416</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T13:38:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Tests depend on bwa
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/10a8ed7018813b6628699b2669b78df57fe67ca9">10a8ed70</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T13:47:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add tmp link for tests for bwa-spades
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/e6badf392a36027797992a2c7e39db6f63a5a6a7">e6badf39</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T14:07:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Spades expects spades-bwa binary, not bwa-spades
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/22ae72c56f0247336dc15b04b5d02ccae627cb29">22ae72c5</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T14:12:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove *.pyc files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/2ee54ae9756a7b8fc20acf629edfe9b54d4f9bf9">2ee54ae9</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T15:29:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch 0118_adjust_spades_home_again.patch replacing 0113_adjust_paths.patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/eec57b9e71f2b7b1b88711a804e724378c12eb9f">eec57b9e</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T16:05:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update override_dh_auto_test: link to data/VERSION files
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/spades/commit/d4bd1d8988a60b6e9129b98133b436534be3f0a7">d4bd1d89</a></strong>
<div>
<span>by Alexandre Mestiashvili</span>
<i>at 2018-09-10T16:19:09Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop PYTHONPATH from wrapper and dh_auto_tests
not needed With correct spades_init.py
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#ac662cc1ae59fb78eca705c0d961f73b99ba5088">
debian/bin/spades
</a>
</li>
<li class="file-stats">
<a href="#8349ebd0c596ef9478eb284b6a482b10861b7531">
debian/links
</a>
</li>
<li class="file-stats">
<a href="#ff3dda2a6b39d356295779453202f6fb12037126">
<span class="new-file">
+
debian/patches/0118_adjust_spades_home_again.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="ac662cc1ae59fb78eca705c0d961f73b99ba5088">
<a href="https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7#ac662cc1ae59fb78eca705c0d961f73b99ba5088"><strong>debian/bin/spades</strong></a>
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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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
</pre>
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<td class="diff-line-num old_line" 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">
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<td class="diff-line-num new_line" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nv" style="color: teal;">SPADESDIR</span><span class="o" style="font-weight: 600;">=</span>/usr/lib/spades/bin</span>
</pre>
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<td class="diff-line-num old old_line" 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
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<td class="diff-line-num new_line 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">
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left right"># </span>SPADESSHARE=/usr/share/spades</span></span>
</pre>
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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="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="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">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">SPADESSHARE</span><span class="o" style="font-weight: 600;">=</span>/usr/share/spades</span>
</pre>
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<td class="diff-line-num old_line" 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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<td class="diff-line-num new_line" 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">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: teal;">exename</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">basename</span> <span class="nv" style="color: teal;">$0</span><span class="sb" style="color: #d14;">`</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
</td>
<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">PATH</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$SPADESDIR</span>:<span class="nv" style="color: teal;">$PATH</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$SPADESDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">exename</span><span class="k" style="font-weight: 600;">}</span>.py <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
</pre>
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</tr>
</table>
<br>
</li>
<li id="8349ebd0c596ef9478eb284b6a482b10861b7531">
<a href="https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7#8349ebd0c596ef9478eb284b6a482b10861b7531"><strong>debian/links</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ usr/bin/spades usr/bin/plasmidspades.py</td>
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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">
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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">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">usr/bin/spades usr/bin/plasmidspades</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">usr/bin/spades usr/bin/rnaspades.py</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">usr/bin/spades usr/bin/rnaspades</span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext">usr/bin/bwa usr/lib/spades/bin/<span class="idiff left right">bwa-spades</span></span>
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<td class="diff-line-num new old_line" data-linenumber="14" 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="13" 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="LC13" class="line" lang="plaintext">usr/bin/bwa usr/lib/spades/bin/<span class="idiff left right">spades-bwa</span></span>
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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">
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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">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">usr/share/man/man1/spades.1.gz /usr/share/man/man1/spades.py.1.gz</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">usr/share/man/man1/dipspades.1.gz /usr/share/man/man1/dipspades.py.1.gz</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz</span>
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<a href="https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7#ff3dda2a6b39d356295779453202f6fb12037126"><strong>debian/patches/0118_adjust_spades_home_again.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="gd" style="color: #000; background-color: #fdd;">--- spades.orig/spades_init.py</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ spades/spades_init.py</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -32,7 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> if isfile(os.path.join(spades_home, 'spades-core')):</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> install_prefix = dirname(spades_home)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> bin_home = join(install_prefix, 'bin')</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- spades_home = join(install_prefix, 'share', 'spades')</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ spades_home = join(install_prefix, '../../', 'share', 'spades')</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> python_modules_home = spades_home</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ext_python_modules_home = spades_home</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7#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">0118_adjust_spades_home_again.patch</span>
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1
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">0002_use_debian_packaged_python-joblib.patch</span>
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2
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">0003_accept-system-bwa.patch</span>
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3
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">0101_cmake_ignore_removed_python-yaml.patch</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +11,6 @@</td>
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10
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"># use-debian-packaged-bamtools.patch ## <<-- does not work - see patch description</span>
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11
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># use-debian-packaged-yaml-cpp.patch ## <<-- does not work - see patch description</span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">0110_build_single_thread.patch</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">0113_adjust_paths.patch</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">0114_use_debian_provided_libs.patch</span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">0115_enable_compiler_messages.patch</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">0111_use_full_config_dirs.patch</span>
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<a href="https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +54,10 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> # Ugly hack to make files available for dh_aut_test and autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> mkdir -p $(CURDIR)/../share/</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> ln -s $(CURDIR)/install_spades/share/spades $(CURDIR)/../share/</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> ln -s /usr/bin/bwa $(CURDIR)/install_spades/bin/spades-bwa</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> $(TMPDIR)/bin/spades.py --test</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> $(TMPDIR)/bin/dipspades.py --test</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> $(TMPDIR)/bin/metaspades.py --test</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,10 +66,14 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> # is still not in the right place. Let's do this later in an</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> # autopkgtest.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"> # $(TMPDIR)/bin/truspades.py --test</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> # Cleunup symlinks</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> rm -rf $(CURDIR)/../share/</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> unlink $(CURDIR)/install_spades/bin/spades-bwa</span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"> echo "Nothing to install"</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> find $(CURDIR) -name *.pyc -delete</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> dh_install</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,6 +84,7 @@ override_dh_install:</td>
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76
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> chmod +x debian/$(DEB_SOURCE)/usr/bin/spades</span>
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77
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> rm -f debian/$(DEB_SOURCE)/usr/share/spades/GPLv2.txt</span>
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78
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"> rm -f debian/$(DEB_SOURCE)/usr/share/spades/LICENSE</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> ln -s ../../../share/spades/VERSION debian/$(DEB_SOURCE)/usr/lib/spades/bin/VERSION</span>
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79
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_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
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">override_dh_installdocs:</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> dh_installdocs</span>
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<a href="https://salsa.debian.org/med-team/spades/compare/3e6039eac2ea4b977d2e53ce09313628853f03fe...d4bd1d8988a60b6e9129b98133b436534be3f0a7#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: run-upstreams-tests<span class="idiff left right"> </span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-upstreams-tests</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @<span class="idiff left right">,bwa</span></span>
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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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