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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/86cdb51ceb37ac51305573d5382165c295f33541">86cdb51c</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-06-03T16:25:32Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update of d/TODO, d/control
</pre>
</li>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/86cdb51ceb37ac51305573d5382165c295f33541#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">@@ -29,7 +29,21 @@ package optitype</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">pyomo</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">Pyomo</span><span class="p">/</span><span class="n" style="color: #333;">pyomo</span></span>
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<td class="diff-line-num new_line old" data-linenumber="32" 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="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">optitype</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">applications</span><span class="p">/</span><span class="n" style="color: #333;">pyomo</span> <span class="p">-</span> <span class="n" style="color: #333;">builds</span> <span class="n" style="color: #333;">locally</span> <span class="p">(</span><span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">does</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">upload</span> <span class="n" style="color: #333;">privileges</span><span class="p">,</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">fail</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">optitype</span></span>
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34
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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="LC35" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">pyutilib</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">PyUtilib</span><span class="p">/</span><span class="n" style="color: #333;">pyutilib</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">modules</span><span class="p">/</span><span class="n" style="color: #333;">pyutilib</span> <span class="p">-</span> <span class="n" style="color: #333;">builds</span><span class="p">,</span> <span class="n" style="color: #333;">tests</span> <span class="n" style="color: #333;">fail</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">pyomo</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">gjh_asl_json</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">ghackebeil</span><span class="p">/</span><span class="n" style="color: #333;">gjh_asl_json</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">pyomo</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">testing</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="s2" style="color: #d14;">"asl solver"</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="mosel"> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">www</span><span class="p">.</span><span class="n" style="color: #333;">ampl</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">netlib</span><span class="p">/</span><span class="n" style="color: #333;">ampl</span><span class="p">/</span><span class="n" style="color: #333;">solvers</span><span class="p">.</span><span class="n" style="color: #333;">tgz</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="mosel"> <span class="n" style="color: #333;">needed</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">gjh_asl_json</span></span>
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33
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="mosel"></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vcfanno</span></span>
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35
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">vcfanno</span></span>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,14 +79,15 @@ package Python module geneimpacts</td>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">python</span><span class="p">-</span><span class="n" style="color: #333;">geneimpacts</span> <span class="p">(</span><span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">queue</span><span class="p">)</span></span>
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66
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="mosel"></span>
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67
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">seqcluster</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">lpantano</span><span class="p">/</span><span class="n" style="color: #333;">seqcluster</span><span class="p">/</span><span class="n" style="color: #333;">archive</span><span class="p">/</span><span class="m" style="color: #099;">1824</span><span class="n" style="color: #333;">d37</span><span class="p">.</span><span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">gz</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="mosel"><span class="idiff left right"> </span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">lpantano</span><span class="p">/</span><span class="n" style="color: #333;">seqcluster</span><span class="p">/</span><span class="n" style="color: #333;">archive</span><span class="p">/</span><span class="m" style="color: #099;">1824</span><span class="n" style="color: #333;">d37</span><span class="p">.</span><span class="n" style="color: #333;">tar</span><span class="p">.</span><span class="n" style="color: #333;">gz</span></span>
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69
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">pizzly</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">pmelsted</span><span class="p">/</span><span class="n" style="color: #333;">pizzly</span></span>
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<td class="diff-line-num old old_line" data-linenumber="72" 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">
72
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<td class="diff-line-num new_line old" data-linenumber="85" 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="LC72" class="line" lang="mosel"><span class="n" style="color: #333;">including</span> <span class="n" style="color: #333;">pizzly_flatten_json</span><span class="p">.</span><span class="n" style="color: #333;">py</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">pmelsted</span><span class="p">/</span><span class="n" style="color: #333;">pizzly</span></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="n" style="color: #333;">including</span> <span class="n" style="color: #333;">pizzly_flatten_json</span><span class="p">.</span><span class="n" style="color: #333;">py</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="mosel"> <span class="n" style="color: #333;">Steffen</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">look</span></span>
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73
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88
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<pre style="margin: 0;"> <span id="LC88" 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="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">vt</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="mosel"><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">atks</span><span class="p">/</span><span class="n" style="color: #333;">vt</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="mosel"><span class="idiff left right"> </span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">atks</span><span class="p">/</span><span class="n" style="color: #333;">vt</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">fgbio</span></span>
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78
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="mosel"> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">github</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">fulcrumgenomics</span><span class="p">/</span><span class="n" style="color: #333;">fgbio</span></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/86cdb51ceb37ac51305573d5382165c295f33541#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -90,6 +90,7 @@ Recommends: bcftools,</td>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> grabix,</span>
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91
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> libvcflib-tools,</span>
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92
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"> macs,</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> python3-geneimpacts,</span>
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93
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"> python3-h5py,</span>
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94
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> pythonpy,</span>
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95
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> rna-star,</span>
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