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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/e07605b598378934e116c207dbcf43775177c1db">e07605b5</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-08-02T16:19:28Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updates while appearing on crash space
</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
</a>
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/e07605b598378934e116c207dbcf43775177c1db#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">@@ -20,47 +20,60 @@ bcbio.</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages already in the New Queue</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="mosel"><span class="s1" style="color: #d14;">package atropos</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/atropos<span class="idiff left right"> (in new queue)</span></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"><span class="s1" style="color: #d14;">package atropos<span class="idiff left right"> (in new queue) (in crash space)</span></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/atropos</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="mosel"><span class="s1" style="color: #d14;">package bamtofastq from biobambam2</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/biobambam2<span class="idiff left right"> (in new queue)</span></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"><span class="s1" style="color: #d14;">package bamtofastq from biobambam2<span class="idiff left right"> (in new queue) (in crash space)</span></span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/biobambam2</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="mosel"><span class="s1" style="color: #d14;">package kallisto (in new queue)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"><span class="s1" style="color: #d14;">package kallisto (in new queue)<span class="idiff left right"> (in crash space)</span></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pizzly</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/pmelsted/pizzly (in new queue)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pizzly (in new queue) (in crash space)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/pmelsted/pizzly</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/pizzly</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="mosel"><span class="s1" style="color: #d14;">package r-wasabi</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/r-pkg-team/r-other-wasabi<span class="idiff left right"> (in new queue)</span></span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"><span class="s1" style="color: #d14;">package r-wasabi<span class="idiff left right"> (in new queue) (in crash space)</span></span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/r-pkg-team/r-other-wasabi</span></span>
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36
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="mosel"><span class="s1" style="color: #d14;">package tophat-recondition</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/cbrueffer/tophat-recondition (in new queue)</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="mosel"><span class="s1" style="color: #d14;">package tophat-recondition (in new queue) (in crash space)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/cbrueffer/tophat-recondition</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/tophat-recondition</span></span>
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39
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="mosel"><span class="s1" style="color: #d14;">package gffread</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/gffread<span class="idiff left right"> (in new queue)</span></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"><span class="s1" style="color: #d14;">package gffread<span class="idiff left right"> (in new queue but FTBFS)</span></span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/gffread</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"><span class="s1" style="color: #d14;">package libjs-scribl (in new queue) (in crash space)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/libjs-scribl</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://chmille4.github.io/Scribl/</span></span>
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<pre style="margin: 0;">+<span id="LC48" 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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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for DFSG-compliance of seqcluster</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"><span class="s1" style="color: #d14;">package cthreadpool (in new queue) (in crash space)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/Pithikos/C-Thread-Pool/blob/master/thpool.h</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by ViennaRNA</span></span>
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43
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="mosel"></span>
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44
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages just waiting for someone addressing the last mile for the upload</span></span>
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45
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="mosel"><span class="s1" style="color: #d14;">-------------------------------------------------------------------------</span></span>
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46
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="mosel"></span>
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47
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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC47" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyomo</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyomo<span class="idiff left right"> (in crash space)</span></span></span>
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48
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/Pyomo/pyomo</span></span>
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<td class="diff-line-num old_line" data-linenumber="49" 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">
49
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<td class="diff-line-num new_line" data-linenumber="60" 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="LC60" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/science-team/pyomo</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="mosel"><span class="s1" style="color: #d14;"> build-deps on pyutilib</span></span>
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50
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by optitype</span></span>
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51
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<td class="diff-line-num new_line" data-linenumber="63" 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="LC63" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Status: Builds if errors in build time tests will be ignored</span></span>
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52
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="mosel"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyutilib</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="mosel"><span class="s1" style="color: #d14;">package pyutilib<span class="idiff left right"> (in crash space)</span></span></span>
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54
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<td class="diff-line-num new_line" data-linenumber="66" 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="LC66" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/PyUtilib/pyutilib</span></span>
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<td class="diff-line-num old_line" data-linenumber="55" 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">
55
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<td class="diff-line-num new_line" data-linenumber="67" 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="LC67" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/python-team/modules/pyutilib</span></span>
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<td class="diff-line-num old_line" data-linenumber="56" 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">
56
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<td class="diff-line-num new_line" data-linenumber="68" 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="LC68" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by pyomo for testing</span></span>
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57
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<td class="diff-line-num new_line" data-linenumber="69" 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="LC69" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Status: Builds if errors in build time tests will be ignored</span></span>
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58
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="mosel"></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="mosel"><span class="s1" style="color: #d14;">package <span class="idiff left right">seqcluster</span></span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/lpantano/seqcluster/<span class="idiff left right">archive/1824d37.tar.gz</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="mosel"><span class="s1" style="color: #d14;">package <span class="idiff left right">python-seqcluster (in crash space)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="72" 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="LC72" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/lpantano/seqcluster/</span></span>
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<td class="diff-line-num old_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/python-seqcluster</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" 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="LC63" 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="LC74" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The Python3 transition seems fine now.</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package needs RNAfold fof the ViennaRNA package for testing. Otherwise it stalls without an error message.</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Dependencies are incomplete / an update wrecked the one immaculate testing.</span></span>
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<pre style="margin: 0;"> <span id="LC77" 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="LC78" 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="LC79" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +82,6 @@ package seqcluster</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel"><span class="s1" style="color: #d14;"> seqcluster 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>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="mosel"><span class="s1" style="color: #d14;"> The package builds with testing if RNAfold of the ViennaRNA package is present. Otherwise it stalls without an error message.</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Additional requirements:</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="mosel"><span class="s1" style="color: #d14;"> python3-dateutils (in new queue)</span></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">@@ -78,41 +90,34 @@ package seqcluster</td>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="mosel"><span class="s1" style="color: #d14;"> And there are R packages that should be recommended at least (from https://github.com/lpantano/seqcluster/blob/master/scripts/install_libraries.R)</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="mosel"><span class="s1" style="color: #d14;"> # We cover all CRAN packages</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="mosel"><span class="s1" style="color: #d14;"> # Most BioC packages are missing - even edgeR ? :</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="mosel"><span class="s1" style="color: #d14;"> r-bioc-edgeR - missing</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="mosel"><span class="s1" style="color: #d14;"> r-bioc-HTSFilter - Depends DESeq and edgeR which both in turn depend locfit which makes all non-free</span></span>
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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;"> r-bioc-DEGreport - all pre-depends except edgeR are in new</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="mosel"><span class="s1" style="color: #d14;"> <span class="idiff left right">apparently optional for bcbio: </span>r-bioc-edgeR - missing</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="mosel"><span class="s1" style="color: #d14;"> <span class="idiff left right">apparently optional for bcbio: </span>r-bioc-HTSFilter - Depends DESeq and edgeR which both in turn depend locfit which makes all non-free</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="mosel"><span class="s1" style="color: #d14;"> <span class="idiff left right">apparently optional for bcbio: </span>r-bioc-DEGreport - all pre-depends except edgeR are in new</span></span>
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84
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;"> # novel packages</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="mosel"><span class="s1" style="color: #d14;"> install.github("hbc/CHBUtils") - Uploaded to new as r-other-chbutils_0.1+git20171026.a226cee-1</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="mosel"><span class="s1" style="color: #d14;"> r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new</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;"> install_github('</span><span class="n" style="color: #333;">rstudio</span><span class="p">/</span><span class="n" style="color: #333;">rmarkdown</span><span class="s1" style="color: #d14;">') -- this may be the same we have from CRAN - not checked</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="mosel"><span class="s1" style="color: #d14;"> <span class="idiff left right">apparently optional for bcbio: </span>install.github("hbc/CHBUtils") - Uploaded to new as r-other-chbutils_0.1+git20171026.a226cee-1</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="mosel"><span class="s1" style="color: #d14;"> <span class="idiff left right">apparently optional for bcbio: </span>r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="mosel"><span class="s1" style="color: #d14;"> <span class="idiff left right">apparently optional for bcbio: </span>install_github('</span><span class="n" style="color: #333;">rstudio</span><span class="p">/</span><span class="n" style="color: #333;">rmarkdown</span><span class="s1" style="color: #d14;">') -- this may be the same we have from CRAN - not checked</span></span>
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88
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="mosel"></span>
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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;">package viennarna</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="mosel"><span class="s1" style="color: #d14;">package viennarna<span class="idiff left right"> (in crash space)</span></span></span>
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90
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ViennaRNA/ViennaRNA</span></span>
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91
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<pre style="margin: 0;"> <span id="LC103" 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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92
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<pre style="margin: 0;"> <span id="LC104" 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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93
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105
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<pre style="margin: 0;"> <span id="LC105" 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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94
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for testing seqcluster.</span></span>
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95
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen revisits ViennaRNA, will update to new upstream version this weekend</span></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Does not compile</span></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="mosel"><span class="s1" style="color: #d14;"> External dependencies</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="mosel"><span class="s1" style="color: #d14;"> json (in Debian, I think, can otherwise be deconfigured)</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="mosel"><span class="s1" style="color: #d14;"> cthreadpool (uploaded)</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="mosel"><span class="s1" style="color: #d14;"> It now mostly compiles.</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Better use current master than release because of erroneous commits of autogenerated files in 2.4.13 release source tree.</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="mosel"></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="mosel"><span class="s1" style="color: #d14;">package cthreadpool (in new queue)</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/Pithikos/C-Thread-Pool/blob/master/thpool.h</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed by ViennaRNA</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Using current master not release because of erroneous commits of autogenerated files in 2.4.13 release source tree.</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Manual removal of folders along instructions in d/copyright</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Python and Perl packages are not functional, yet, not needed for seqcluster</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Waiting for acceptance of cthreadpool.</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="mosel"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="mosel"><span class="s1" style="color: #d14;">Package MutliQC - (in crash space)</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/multiqc</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Not redistributable until we have removed the highcharts library from that source tree</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ewels/MultiQC/issues/800</span></span>
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106
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="mosel"></span>
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107
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages presumed easy to package</span></span>
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108
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------</span></span>
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109
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="mosel"></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="mosel"><span class="s1" style="color: #d14;">package Scribl</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://chmille4.github.io/Scribl/</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" 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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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Needed for seqcluster</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="mosel"><span class="s1" style="color: #d14;"> In new queue as libjs-scribl</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="mosel"></span>
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116
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="mosel"><span class="s1" style="color: #d14;">package gjh_asl_json</span></span>
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117
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://github.com/ghackebeil/gjh_asl_json</span></span>
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118
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by pyomo for testing</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" 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="130" 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">@@ -125,10 +130,6 @@ package "asl solver"</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://www.ampl.com/netlib/ampl/solvers.tgz</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="mosel"><span class="s1" style="color: #d14;"> needed by gjh_asl_json</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="mosel"></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="mosel"><span class="s1" style="color: #d14;">Package MutliQC - in salsa</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/multiqc</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Steffen will address this one</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="mosel"></span>
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132
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="mosel"><span class="s1" style="color: #d14;">r-bioc-edgeR</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://tracker.debian.org/pkg/r-bioc-edger</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This was removed from buster in February - a bit of a bummer, I tend to think</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" 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="212" 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">@@ -211,7 +212,7 @@ package fgbio</td>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Anyone much into scala?</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="mosel"><span class="s1" style="color: #d14;">package manta</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="mosel"><span class="s1" style="color: #d14;">https://github.com/Illumina/manta/</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="mosel"><span class="s1" style="color: #d14;"><span class="idiff left right"> </span>https://github.com/Illumina/manta/</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/manta</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="mosel"><span class="s1" style="color: #d14;">package strelka</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" 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="234" 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">@@ -233,5 +234,5 @@ Packages no longer used by bcbio</td>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="mosel"><span class="s1" style="color: #d14;">--------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="mosel"><span class="s1" style="color: #d14;">package lumpy</span></span>
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<td class="diff-line-num old old_line" data-linenumber="236" 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="LC236" class="line" lang="mosel"><span class="s1" style="color: #d14;">https://github.com/arq5x/lumpy-sv</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="mosel"><span class="s1" style="color: #d14;"><span class="idiff left right"> </span>https://github.com/arq5x/lumpy-sv</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="mosel"></span></pre>
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