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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/megahit">Debian Med / megahit</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/megahit/commit/23d414fc452a7f42e53e50b8e5395aeef9861c66">23d414fc</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-10-15T05:08:50Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change test data path to directory where wrapper was invoked
Todo: Currently the python data file check was removed as this became problematic for me, but re-add to ensure no errornous outcome
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<strong><a href="https://salsa.debian.org/med-team/megahit/commit/0b3b25e8b17b1fa87c002a8aa364584e8ba7ccba">0b3b25e8</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-10-15T05:10:11Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install files into their correct directories
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<h4>3 changed files:</h4>
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<a href="#6099be245ede8b65d332ffa57b1831bb7f575907">
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debian/megahit.install
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<li class="file-stats">
<a href="#9aeb3f33ba7407966ded6269d14de4bad9117663">
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debian/patches/fix_test_path.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="6099be245ede8b65d332ffa57b1831bb7f575907">
<a href="https://salsa.debian.org/med-team/megahit/compare/9bfa748d42ea907f0ce283dbfdc32b95048f96e5...0b3b25e8b17b1fa87c002a8aa364584e8ba7ccba#6099be245ede8b65d332ffa57b1831bb7f575907"><strong>debian/megahit.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">obj</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x86_64</span><span class="o" style="font-weight: 600;">-</span><span class="nx">linux</span><span class="o" style="font-weight: 600;">-</span><span class="nx">gnu</span><span class="o" style="font-weight: 600;">/</span><span class="nx">megahit</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">obj</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x86_64</span><span class="o" style="font-weight: 600;">-</span><span class="nx">linux</span><span class="o" style="font-weight: 600;">-</span><span class="nx">gnu</span><span class="o" style="font-weight: 600;">/</span><span class="nx">megahit_core</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="nx">obj</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x86_64</span><span class="o" style="font-weight: 600;">-</span><span class="nx">linux</span><span class="o" style="font-weight: 600;">-</span><span class="nx">gnu</span><span class="o" style="font-weight: 600;">/</span><span class="nx">megahit_core_no_hw_accel</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">obj</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x86_64</span><span class="o" style="font-weight: 600;">-</span><span class="nx">linux</span><span class="o" style="font-weight: 600;">-</span><span class="nx">gnu</span><span class="o" style="font-weight: 600;">/</span><span class="nx">megahit_core_popcnt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">obj</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x86_64</span><span class="o" style="font-weight: 600;">-</span><span class="nx">linux</span><span class="o" style="font-weight: 600;">-</span><span class="nx">gnu</span><span class="o" style="font-weight: 600;">/</span><span class="nx">megahit_toolkit</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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<li id="9aeb3f33ba7407966ded6269d14de4bad9117663">
<a href="https://salsa.debian.org/med-team/megahit/compare/9bfa748d42ea907f0ce283dbfdc32b95048f96e5...0b3b25e8b17b1fa87c002a8aa364584e8ba7ccba#9aeb3f33ba7407966ded6269d14de4bad9117663"><strong>debian/patches/fix_test_path.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: for sake of autopkgtest, change test data directory</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> This now becomes the working 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: 2019-10-15</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: megahit/src/megahit</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;">--- megahit.orig/src/megahit 2019-10-15 06:06:49.207438632 +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;">+++ megahit/src/megahit 2019-10-15 06:06:49.203438593 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">@@ -566,14 +566,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> def find_test_data_path():</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- script_path = software_info.script_path</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for path in [os.path.join(script_path, '..'), os.path.join(script_path, '../share/megahit')]:</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- test_data_dir = abspath(os.path.join(path, 'test_data'))</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if os.path.isdir(test_data_dir) and all(</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- f in os.listdir(test_data_dir) for f in ['r1.il.fa.gz', 'r2.il.fa.bz2', 'r3_1.fa', 'r3_2.fa', 'r4.fa']):</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return test_data_dir</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise Usage('Test data not found! Script path = {0}'.format(script_path))</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ # The test will suspend anyways if the files are not there</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;">+ test_data_dir = '.'</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ return test_data_dir</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> def check_reads():</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> if opt.test_mode:</span></pre>
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<a href="https://salsa.debian.org/med-team/megahit/compare/9bfa748d42ea907f0ce283dbfdc32b95048f96e5...0b3b25e8b17b1fa87c002a8aa364584e8ba7ccba#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fix_test_path.patch</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">2to3.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">fix_src_packed_field.patch</span></pre>
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