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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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<ul>
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<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/a785f732a7d94ddc1c350a36736216724fab29d3">a785f732</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-06-19T22:28:49Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Wording, Steffen revisits seqcluster
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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/a785f732a7d94ddc1c350a36736216724fab29d3#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">@@ -2,11 +2,15 @@ TODO for bcbio with Debian</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="p">==========================</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"><span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">following</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">list</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">packages</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">used</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">at</span> <span class="n" style="color: #333;">least</span> <span class="n" style="color: #333;">one</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span></span>
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5
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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">workflows</span> <span class="n" style="color: #333;"><span class="idiff left right">it</span></span> <span class="n" style="color: #333;">aggregates</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">complete</span> <span class="n" style="color: #333;">coverage</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">Debian</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">tools</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">workflows</span> <span class="n" style="color: #333;"><span class="idiff left right">bcbio</span></span> <span class="n" style="color: #333;">aggregates</span><span class="p">.</span> <span class="n" style="color: #333;">A</span> <span class="n" style="color: #333;">complete</span> <span class="n" style="color: #333;">coverage</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">Debian</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">all</span> <span class="n" style="color: #333;">these</span> <span class="n" style="color: #333;">tools</span></span>
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6
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="mosel"><span class="n" style="color: #333;">seems</span> <span class="n" style="color: #333;">increasingly</span> <span class="n" style="color: #333;">unlikely</span> <span class="p">-</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">packaging</span> <span class="n" style="color: #333;">would</span> <span class="n" style="color: #333;">take</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">than</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">tools</span> <span class="n" style="color: #333;">scientific</span> <span class="n" style="color: #333;">lifespan</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">.</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">generation</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">problem</span> <span class="n" style="color: #333;">solving</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">tools</span><span class="s1" style="color: #d14;"><span class="idiff left right">'</span> scientific lifespan, i.e. there is a new generation of problem solving</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"><span class="s1" style="color: #d14;">emerging and/or the workflow as a whole will have mutated in the meantime.</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="s1" style="color: #d14;">We yet have to find an answer to this challenge. For quite some this is to</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="s1" style="color: #d14;">just go and use Conda. We should also consider mixing Conda with Debian,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"><span class="s1" style="color: #d14;">though. But let us first see where we are with bcbio:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages already accepted</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"><span class="s1" style="color: #d14;">------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"></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">@@ -64,6 +68,7 @@ package seqcluster</td>
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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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66
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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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67
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="mosel"></span>
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68
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="mosel"></span>
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69
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74
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<pre style="margin: 0;"> <span id="LC74" 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 unfold js-unfold old_line" data-linenumber="87" 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>
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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">@@ -87,8 +92,8 @@ Package MutliQC - in salsa</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="mosel"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="mosel"><span class="n" style="color: #333;">Packages</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">importance</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">basic</span> <span class="n" style="color: #333;">NGS</span> <span class="n" style="color: #333;">workflow</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">well</span></span> <span class="n" style="color: #333;">beyond</span> <span class="n" style="color: #333;">bcbio</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="mosel"><span class="p">---------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="mosel"><span class="s1" style="color: #d14;">Packages of importance for basic NGS workflow<span class="idiff left right">s with motivation</span> beyond bcbio</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="mosel"><span class="s1" style="color: #d14;">---------------------------------------------------------------<span class="idiff left right">------------</span></span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="mosel"><span class="s1" style="color: #d14;">package mosdepth</span></span>
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94
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="mosel"><span class="s1" style="color: #d14;"> https://salsa.debian.org/med-team/mosdepth</span></span>
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