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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcalm">Debian Med / bcalm</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcalm/commit/700890df208d1f947781fbf17c1fde24262ebc09">700890df</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-23T10:57:49Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch to fix the test scripts to use the correct binary
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
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+
debian/patches/fix_tests.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70">
<a href="https://salsa.debian.org/med-team/bcalm/commit/700890df208d1f947781fbf17c1fde24262ebc09#5d4bc5bec9cccce49eb00b14a49d6fa0feedbf70"><strong>debian/patches/fix_tests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: force test scripts to use /usr/bin/bcalm</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> Use /usr/bin/bcalm and not the binary in the build directory.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Shayan Doust <hello@shayandoust.me></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2019-09-23</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">---</span></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">Index: bcalm/example/run-tiny.sh</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcalm.orig/example/run-tiny.sh 2019-09-23 11:55:25.936891862 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcalm/example/run-tiny.sh 2019-09-23 11:55:25.928891770 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -1,2 +1 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-bcalm=`find ../*/bcalm | head -n 1` # covers bin/ and build/ cases</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-$bcalm -in tiny_read.fa -kmer-size 13 -abundance-min 1 $1 $2</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bcalm -in tiny_read.fa -kmer-size 13 -abundance-min 1 $1 $2</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gh" style="color: #999;">Index: bcalm/example/circular_unitigs_unittests/CMD</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bcalm.orig/example/circular_unitigs_unittests/CMD 2019-09-23 11:55:25.936891862 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bcalm/example/circular_unitigs_unittests/CMD 2019-09-23 11:55:25.928891770 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> #!/bin/bash</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if [ "$1" == "3" ]</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> then</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ../../build/bcalm -in test3.fa -kmer-size 7 -abundance-min 1 -minimizer-size 5</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bcalm -in test3.fa -kmer-size 7 -abundance-min 1 -minimizer-size 5</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> exit 0</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> fi</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-../../build/bcalm -in test1.fa -kmer-size 7 -abundance-min 1 -minimizer-size 5</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+bcalm -in test1.fa -kmer-size 7 -abundance-min 1 -minimizer-size 5</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/bcalm/commit/700890df208d1f947781fbf17c1fde24262ebc09#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_tests.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">modify_cmake.patch</span></pre>
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