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<h3>
Michael R. Crusoe 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/d9e2b213d053cd3071fde18f521f7130cd609da0">d9e2b213</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T08:40:50Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/d44333413b59d7e3e2517665c89a168944750d8d">d4433341</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T08:41:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.1.3'
Update to upstream version '1.1.3'
with Debian dir 66b4b7739104633ad67c5c4511f4d60bbbd50333</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/8d2a4655c9667033197722fbe20102582fee6398">8d2a4655</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T08:42:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/5d78e887138135274bbb4989af2f60c704934b38">5d78e887</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T08:45:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/python3.patch: removed, applied upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/b2ff8b839bb06eaf2f08ae27388c2c31fe25a3bd">b2ff8b83</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T08:55:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add ${sphinxdoc:Built-Using} to -doc
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/0b8fbcfe450a32be6bf300faa6a07e26e4ccab0d">0b8fbcfe</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T09:07:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes a few spelling errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/63353604fecedcfef1690e3af5d6ee589a6a44ea">63353604</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T09:07:58Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add pytest to enable running the tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/f188722ae030378ed2cdbff7d63f1484da185827">f188722a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-10T09:07:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">python3-bcbio: section is "python"
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/7b98f981e77e80d109e7b14e4cacc2e544a480a1">7b98f981</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-02-11T07:13:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add recommendations discovered through testing
and make a list of software that needs packaging
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
</a>
</li>
<li class="file-stats">
<a href="#d30b04166486087de34ff05cf278d3dd2ddd2360">
HISTORY.md
</a>
</li>
<li class="file-stats">
<a href="#059a93c69080af2f6054c5324203b7af73cc5b83">
bcbio/bam/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#e2a5482df2cfb77e36bb48de8be98a8a2778fe28">
bcbio/bam/callable.py
</a>
</li>
<li class="file-stats">
<a href="#ffb2e540c7c7301c64659d69a0b5cbc3e9da66b1">
bcbio/bam/cram.py
</a>
</li>
<li class="file-stats">
<a href="#182fba4769123c455cd02418f79d193a381ad1c4">
bcbio/bam/fastq.py
</a>
</li>
<li class="file-stats">
<a href="#e518229f249f53b16d0dd891314f18afa565e3cb">
bcbio/broad/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#2d356a30008ed932f27e4ace4ff645a2231fa5de">
bcbio/cwl/create.py
</a>
</li>
<li class="file-stats">
<a href="#9d1b2d9542eb07c5b8d3680169848427c1e5d46d">
bcbio/cwl/cwlutils.py
</a>
</li>
<li class="file-stats">
<a href="#f6af6837df6254f77d2faec43d98066631097b5e">
bcbio/cwl/defs.py
</a>
</li>
<li class="file-stats">
<a href="#1b659f58ae5c6fb1faeab633dcdd75182ee896da">
bcbio/cwl/hpc.py
</a>
</li>
<li class="file-stats">
<a href="#3fe38e0e6f6bb2fb451c38b6cd908de9ba5992b2">
bcbio/cwl/tool.py
</a>
</li>
<li class="file-stats">
<a href="#86f5e930c36509ffef1d2e158fda6d89e6b19e5f">
bcbio/cwl/workflow.py
</a>
</li>
<li class="file-stats">
<a href="#c0ecce57df96b673f49298e6860ec8ad7721052b">
bcbio/distributed/multi.py
</a>
</li>
<li class="file-stats">
<a href="#38ff5538b3a22e59bc372950e834f4a596a51bce">
bcbio/distributed/objectstore.py
</a>
</li>
<li class="file-stats">
<a href="#5ec8cfcc8dade2381e602fdfdb8058cd5023f27c">
bcbio/distributed/resources.py
</a>
</li>
<li class="file-stats">
<a href="#24b10c4075c91fa8a08a9bf38d2e3451b81a5fb7">
bcbio/distributed/runfn.py
</a>
</li>
<li class="file-stats">
<a href="#dbbe91ea0088679bb3e908a76b4a644641bdb697">
bcbio/distributed/split.py
</a>
</li>
<li class="file-stats">
<a href="#18ba3acc4e00e0fa51a6e70346cfe890d566f248">
bcbio/galaxy/api.py
</a>
</li>
<li class="file-stats">
<a href="#7f8e86644b62bf131a07b434c1d1f5892bce0ae6">
bcbio/galaxy/nglims.py
</a>
</li>
<li class="file-stats">
<a href="#b0b4ca14d5e83a5d8319655cff8263ee855dddfa">
bcbio/graph/graph.py
</a>
</li>
<li class="file-stats">
<a href="#cd08dceb71bc9bd7ab94728fc3f310e15324b176">
bcbio/heterogeneity/bubbletree.py
</a>
</li>
<li class="file-stats">
<a href="#fee19f4f498a2b34eca43fa79376fa526f252577">
bcbio/heterogeneity/chromhacks.py
</a>
</li>
<li class="file-stats">
<a href="#399d062423d7dfda6c87b58e34ead968ccd6189c">
bcbio/heterogeneity/loh.py
</a>
</li>
<li class="file-stats">
<a href="#2c41f66e6b62c219ea3dacf88e29bb91c70110ce">
bcbio/hla/bwakit.py
</a>
</li>
<li class="file-stats">
<a href="#1ef80d5e67c000a5c2448e6dc3b7c172e118b794">
bcbio/illumina/flowcell.py
</a>
</li>
<li class="file-stats">
<a href="#183c8f99ac39f0fb348d40a8735debf81dc423ec">
bcbio/illumina/machine.py
</a>
</li>
<li class="file-stats">
<a href="#8779489a282644a9d76cbfa2ef65b251ba8634bc">
bcbio/illumina/samplesheet.py
</a>
</li>
<li class="file-stats">
<a href="#c2c95c1c2c7ebc5cc8a22213d7dffe23e9aca3c9">
bcbio/illumina/transfer.py
</a>
</li>
<li class="file-stats">
<a href="#cb1999524a51a97bd40da890cd301d883550f995">
bcbio/install.py
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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<p style="font-size: small; color: #777777;">
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