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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/e52b151133c3af226fb80401eb54497bfa1c4e87">e52b1511</a></strong>
<div>
<span>by Steffen Möller</span>
<i>at 2019-03-21T13:55:21Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update for newly packaged StringTie
</pre>
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<h4>3 changed files:</h4>
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<li class="file-stats">
<a href="#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
debian/TODO
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba">
<a href="https://salsa.debian.org/med-team/bcbio/commit/e52b151133c3af226fb80401eb54497bfa1c4e87#d9d67e646e83973f5e1d6cd63fe8c9dffb33ebba"><strong>debian/TODO</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" 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">@@ -37,9 +37,7 @@ https://github.com/ewels/MultiQC</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">sailfish</span></span>
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<pre style="margin: 0;"> <span id="LC38" 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;">kingsfordgroup</span><span class="p">/</span><span class="n" style="color: #333;">sailfish</span></span>
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39
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39
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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;">stringtie</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;">http</span><span class="p">://</span><span class="n" style="color: #333;">ccb</span><span class="p">.</span><span class="n" style="color: #333;">jhu</span><span class="p">.</span><span class="n" style="color: #333;">edu</span><span class="p">/</span><span class="n" style="color: #333;">software</span><span class="p">/</span><span class="n" style="color: #333;">stringtie</span><span class="p">/</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;">http</span><span class="p">://</span><span class="n" style="color: #333;">ccb</span><span class="p">.</span><span class="n" style="color: #333;">jhu</span><span class="p">.</span><span class="n" style="color: #333;">edu</span><span class="p">/</span><span class="n" style="color: #333;">software</span><span class="p">/</span><span class="n" style="color: #333;">stringtie</span><span class="p">/</span><span class="n" style="color: #333;">dl</span><span class="p">/</span><span class="n" style="color: #333;">stringtie</span><span class="p">-</span><span class="m" style="color: #099;">1.3.5</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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40
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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;">stringtie</span> <span class="p">-</span> <span class="n" style="color: #333;">done</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">bugs</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;">cgi</span><span class="p">-</span><span class="n" style="color: #333;">bin</span><span class="p">/</span><span class="n" style="color: #333;">bugreport</span><span class="p">.</span><span class="n" style="color: #333;">cgi</span><span class="p">?</span><span class="n" style="color: #333;">bug</span><span class="p">=</span><span class="m" style="color: #099;">924101</span></span>
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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="LC42" class="line" lang="mosel"><span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">kallisto</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/e52b151133c3af226fb80401eb54497bfa1c4e87#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bcbio (1.1.3-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio (1.1.3-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream release.</span>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/e52b151133c3af226fb80401eb54497bfa1c4e87#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">@@ -77,10 +77,14 @@ Recommends: bcftools,</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> sambamba,</span>
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> samblaster,</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> samtools,</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> salmon,</span>
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80
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> subread,</span>
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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
81
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> tabix,</span>
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82
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> wget</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">Suggests: toil, cwltool,</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">Suggests: toil,</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> cwltool,</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="plaintext"> stringtie,</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> kallisto,</span>
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84
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"> bcbio-doc</span>
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85
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">Description: toolkit for analysing high-throughput sequencing data</span>
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86
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> This package installs the command line tools of the bcbio-nextgen</span>
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