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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/0cd543d3cc66fa1bc70dc90a9b82b894478c2eac">0cd543d3</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-06-20T10:13:05Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">seqcluster needs ViennaRNA
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<h4>1 changed file:</h4>
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<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/0cd543d3cc66fa1bc70dc90a9b82b894478c2eac#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</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">@@ -65,15 +65,29 @@ package pyutilib</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="mosel"><span class="s1" style="color: #d14;">package seqcluster</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/python-seqcluster</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Some nitty-gritty was going on there wrt Python3 transition</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="mosel"><span class="s1" style="color: #d14;"> and an upcoming new release. Needs another review and</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="mosel"><span class="s1" style="color: #d14;"> likely some communication with upstream.</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen addresses this.</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The Python3 transition seems fine now. Weird, though,</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="mosel"><span class="s1" style="color: #d14;"> the test takes too long / something hangs.</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="mosel"><span class="s1" style="color: #d14;"> When grepping for "conda install":</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ./doc/source/installation.rst: ~/install/seqcluster/anaconda/conda install seqcluster seqbuster bedtools samtools pip nose numpy scipy pandas pyvcf -c bioconda</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ./Dockerfile: conda install --yes -c conda-forge -c bioconda scipy seqcluster bedtools samtools pip nose setuptools -q && \</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ./.travis.yml:- conda install --yes -c conda-forge -c bioconda memory_profiler openjdk pysam pybedtools pandas numpy biopython progressbar2 pyyaml bedtools samtools mirtop viennarna -q</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="mosel"><span class="s1" style="color: #d14;"> so, for some successful testing it seems like we need viennarna, still. That is not yet in the distribution. If truly dependending on it then bcbio ends up in contrib.</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;">package viennarna</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ViennaRNA/ViennaRNA</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="mosel"><span class="s1" style="color: #d14;"> No idea about where exactly we stand with this.</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package now has a custom license file - redistributable but non-free.</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for testing seqcluster.</span></span>
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<td class="diff-line-num old_line" data-linenumber="73" 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">
73
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="74" 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">
74
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages presumed easy to package</span></span>
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<td class="diff-line-num old_line" data-linenumber="75" 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">
75
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<td class="diff-line-num 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">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------</span></span>
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76
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;">package Scribl</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://chmille4.github.io/Scribl/</span></span>
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<td class="diff-line-num new old_line" data-linenumber="77" 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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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="mosel"><span class="s1" style="color: #d14;"> A surprisingly neat JavaScript library to show genomic features</span></span>
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<td class="diff-line-num new old_line" data-linenumber="77" 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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for seqcluster</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"></span>
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77
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="mosel"><span class="s1" style="color: #d14;">package gjh_asl_json</span></span>
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<td class="diff-line-num old_line" data-linenumber="78" 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">
78
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ghackebeil/gjh_asl_json</span></span>
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<td class="diff-line-num old_line" data-linenumber="79" 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">
79
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by pyomo for testing</span></span>
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