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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/a48982aa7bca71129decc931487c09ef30496119">a48982aa</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-12-13T15:24:43+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">TL;DR for d/TODO
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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/a48982aa7bca71129decc931487c09ef30496119#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="mosel"><span class="n" style="color: #333;">TODO</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">bcbio</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">Debian</span></span>
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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;">TL</span><span class="p">;</span><span class="n" style="color: #333;">DR</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="p">-----</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="mosel"><span class="n" style="color: #333;">We</span> <span class="n" style="color: #333;">yet</span> <span class="n" style="color: #333;">fail</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">bcbio</span> <span class="n" style="color: #333;">workflows</span> <span class="n" style="color: #333;">successfully</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">builds</span> <span class="n" style="color: #333;">but</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">fail</span><span class="p">.</span> <span class="n" style="color: #333;">You</span> <span class="n" style="color: #333;">get</span> <span class="n" style="color: #333;">pretty</span> <span class="n" style="color: #333;">close</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">installing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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="LC9" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">GATK</span> <span class="p">(</span><span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">Java</span> <span class="n" style="color: #333;">dependencies</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">packaged</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">qualimap</span> <span class="p">(</span><span class="n" style="color: #333;">sources</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Java</span> <span class="n" style="color: #333;">dependencies</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">available</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="mosel"><span class="n" style="color: #333;">manually</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">immediate</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">we</span> <span class="n" style="color: #333;">suggest</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">install</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="mosel"><span class="n" style="color: #333;">bcbio</span> <span class="n" style="color: #333;">via</span> <span class="n" style="color: #333;">conda</span> <span class="p">-</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">cordially</span> <span class="n" style="color: #333;">invite</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">help</span> <span class="n" style="color: #333;">us</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">bringing</span> <span class="n" style="color: #333;">bcbio</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="mosel"><span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">Debian</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="mosel"><span class="k" style="font-weight: 600;">IF</span> <span class="n" style="color: #333;">YOU</span> <span class="n" style="color: #333;">ARE</span> <span class="n" style="color: #333;">READING</span> <span class="n" style="color: #333;">THIS</span> <span class="k" style="font-weight: 600;">AND</span> <span class="n" style="color: #333;">FEEL</span> <span class="n" style="color: #333;">LIKE</span> <span class="n" style="color: #333;">HELPING</span> <span class="n" style="color: #333;">OUT</span> <span class="p">-</span> <span class="n" style="color: #333;">PLEASE</span> <span class="n" style="color: #333;">CONTACT</span> <span class="n" style="color: #333;">US</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"><span class="p">---------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"></span>
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