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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/ec6be7565d7ee33bca8bb1203e654049e4e1f2f8">ec6be756</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-06-27T10:58:04Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update seqcluster loses amcharts
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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/ec6be7565d7ee33bca8bb1203e654049e4e1f2f8#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +75,7 @@ package seqcluster</td>
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<pre style="margin: 0;"> <span id="LC75" 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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<td class="diff-line-num old_line" data-linenumber="76" 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="LC76" 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="LC77" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="78" 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="LC78" class="line" lang="mosel"><span class="s1" style="color: #d14;"> seqcluster <span class="idiff left right">redistributes a "Free as in beer" graph library in its source tree at ./misc/js/amcharts.js that upstream accepts to be substituted with references to the online location in a CDN. Steffen will address that. Downside of it all: seqcluster needs to go to contrib</span>.</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="mosel"><span class="s1" style="color: #d14;"> seqcluster <span class="idiff left right">accepted a patch to eliminate a "Free as in beer" graph library from its source tree at ./misc/js/amcharts.js. These are now references to the online location in a CDN</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Additional requirements:</span></span>
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<td class="diff-line-num old_line" data-linenumber="81" 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="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;"> python3-dateutils (not yet packaged)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" 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="113" 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">@@ -113,6 +113,7 @@ package Scribl</td>
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<pre style="margin: 0;"> <span id="LC113" 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 old_line" data-linenumber="114" 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="LC114" 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 old_line" data-linenumber="115" 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="LC115" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for seqcluster</span></span>
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<td class="diff-line-num new old_line" data-linenumber="116" 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="116" 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="LC116" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen addresses packaging this JS library from 2012</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="mosel"><span class="s1" style="color: #d14;">package gjh_asl_json</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ghackebeil/gjh_asl_json</span></span>
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