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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>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/8f89a482445462bd67b9c6fbea0d567fac72232a">8f89a482</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-10-12T14:36:42+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Attempt to fix STAR test error
</pre>
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<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/f842ea4f811399ea6e2cff67b4d377e0cdf34c29">f842ea4f</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-10-12T15:16:49+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">skip the STAR DTU test until a better fix is found
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<li>
<strong><a href="https://salsa.debian.org/med-team/trinityrnaseq/-/commit/56b1eb8ab745ac57b084cc8e8772e68afccf912a">56b1eb8a</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-10-12T15:17:04+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release 2.11.0+dfsg-2
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<h4>4 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#2d23b99ac647f3c9f82068b1bb3d6cd3cf9243e7">
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debian/patches/STAR_genomeSAindexNbases
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<a href="#b8b51d78ba9d08ba6ad2d4462a0455f0e5a63c9c">
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debian/patches/skip_DTU_STAR_test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346...56b1eb8ab745ac57b084cc8e8772e68afccf912a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trinityrnaseq (2.11.0+dfsg-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debian/patches/STAR_genomeSAindexNbases: Attempt to fix the DTU STAR test error</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debian/patches/skip_DTU_STAR_test: skip the test until a better fix is</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> found</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <crusoe@debian.org> Mon, 12 Oct 2020 15:16:52 +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">trinityrnaseq (2.11.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<li id="2d23b99ac647f3c9f82068b1bb3d6cd3cf9243e7">
<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346...56b1eb8ab745ac57b084cc8e8772e68afccf912a#2d23b99ac647f3c9f82068b1bb3d6cd3cf9243e7"><strong>debian/patches/STAR_genomeSAindexNbases</strong></a>
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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>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Implement genomeSAindexNbases</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/trinityrnaseq/trinityrnaseq/issues/905#issuecomment-707094332</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/util/misc/run_STAR_via_samples_file.pl</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/util/misc/run_STAR_via_samples_file.pl</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -88,6 +88,7 @@</span></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>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> my $genomeChrBinNbits = min(18, int(log((-s $genome) / $num_contigs) / log(2) + 0.5) );</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;">+ my $genomeSAindexNbases = int(log(-s $genome) / log(2) / 2) - 1;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> my @read_sets = &parse_samples_file($samples_file); </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"><span class="p">@@ -102,6 +103,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> my $cmd = "$star_prog --runThreadN $CPU --runMode genomeGenerate --genomeDir $star_index "</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> . " --genomeFastaFiles $genome "</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> . " --genomeChrBinNbits $genomeChrBinNbits "</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;">+ . " --genomeSAindexNbases $genomeSAindexNbases "</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> . " --limitGenomeGenerateRAM 40419136213 ";</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> if ($gtf_file) {</span></pre>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346...56b1eb8ab745ac57b084cc8e8772e68afccf912a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">STAR_genomeSAindexNbases</span>
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1
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">butterfly</span>
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2
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">jellyfish-path</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">update-paths</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">@@ -18,3 +19,4 @@ submake</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">skip_blat</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">fix-gcc-10.patch</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">bamsifter_build</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">skip_DTU_STAR_test</span></pre>
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<a href="https://salsa.debian.org/med-team/trinityrnaseq/-/compare/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346...56b1eb8ab745ac57b084cc8e8772e68afccf912a#b8b51d78ba9d08ba6ad2d4462a0455f0e5a63c9c"><strong>debian/patches/skip_DTU_STAR_test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Skip the STAR based DTU tests for now</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>
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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/test_DTU/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/test_DTU/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -1,5 +1,5 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> test:</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;">- ./runMe.sh STAR</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #./runMe.sh STAR</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> ./runMe.sh HISAT2</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> clean:</span></pre>
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