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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/toil">Debian Med / toil</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/ee60b8372c13b191ccb7fd6ecb62dc9d6affc87c">ee60b837</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T10:04:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">skip galaxy-lib, not yet packaged for Debian
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/6302fee8653ba0c0d30cd8d089afdb5ebe2837e0">6302fee8</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T10:31:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix doc build
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/1f2f49b3041468181f122c21e9ebfe61fca77ea8">1f2f49b3</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T10:47:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjust docs for a Debian installed Toil.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/cf9246325f7fdf2f1531b50692212932ae035bf5">cf924632</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T10:52:51Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">more missing deps
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/46d02fb72358d33f4a73f83ba4b22d46ec8ecb04">46d02fb7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T10:54:53Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.18.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/6d56cbba1527c2d398f410acbcee7bf22e670442">6d56cbba</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T10:55:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.18.0'
Update to upstream version '3.18.0'
with Debian dir edf8f711b582380aed6ca6f96befa1ceeb8b18e2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/1689c77026ce577d63dca80a04636cfb648fab19">1689c770</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T11:07:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patches for 3.18.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/32dd207a8d687184e1b14d0e65f4554f3e6dfd2e">32dd207a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T11:13:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">try building for Python 3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/1e5a132b55e051efcdbe864ba6ca70b0a3a472e7">1e5a132b</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T11:19:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cgcloud is no longer needed (moved into Toil itself).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/009d8c477bdb6c53a5c8fb81c2523e19c0e0fdcc">009d8c47</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T12:22:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">adjust to newer cwltool
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/37d9aed953d961a2f197ed17de8e8ea7680d681c">37d9aed9</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T12:26:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't ship cwltoil, use toil-cwl-runner instead.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/cd3bade7771dfaea6b1c577ae8a8f8f42deb3255">cd3bade7</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T12:35:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">better document the patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/toil/commit/dc9c65671624eef6b331259c906cf34714492a5f">dc9c6567</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2019-01-07T12:46:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling.
</pre>
</li>
</ul>
<h4>30 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#083a75879f75eab7b4cd4116aad6215c5988ac76">
attic/toil-sort-example.py
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#f5f51601866c86e59a004bd93fa415f5675be8c5">
debian/clean
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#17f59bf2814bb5df9051cfdd9d5798e79655e9fe">
<span class="new-file">
+
debian/patches/adjust_to_newer_cwltool
</span>
</a>
</li>
<li class="file-stats">
<a href="#43bce5830afffd9cb2acc8dc5edc5294f813bf08">
<span class="new-file">
+
debian/patches/debianize_docs
</span>
</a>
</li>
<li class="file-stats">
<a href="#e94fbb8719c4a68a67df894f2683205bb9914852">
<span class="new-file">
+
debian/patches/no_galaxy_lib
</span>
</a>
</li>
<li class="file-stats">
<a href="#e4edc1d4104bcf89de6479329e0a1f666d285d01">
debian/patches/no_virtualenv_to_create_manpages.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#bbcb48e2be151813ceeaaec7eadcaf824b49c1c6">
debian/patches/setting_version.patch
</a>
</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
</span>
</a>
</li>
<li class="file-stats">
<a href="#cb805f74cef9b2dafa0758f976c0bcadda0b7dde">
debian/patches/version.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#f99c72d2aacbf31ded1872c66de3f988dced0301">
docs/appendices/environment_vars.rst
</a>
</li>
<li class="file-stats">
<a href="#abd8589b4d5ee2ea66ee95d8caf4e8759ffb9ce0">
docs/contributing/contributing.rst
</a>
</li>
<li class="file-stats">
<a href="#5e25feb6b25012c00d6a27af4470f92ec5ccb67b">
docs/developingWorkflows/developing.rst
</a>
</li>
<li class="file-stats">
<a href="#9b7b19eaf87ceb524470a920a457425b602cd816">
docs/developingWorkflows/toilAPIBatchsystem.rst
</a>
</li>
<li class="file-stats">
<a href="#cb9729d9831b9bd58e9bb638cc0c36e12ae1d1c1">
docs/developingWorkflows/toilAPIFilestore.rst
</a>
</li>
<li class="file-stats">
<a href="#9c7786e2c4730fab23a42468d049ec242c297b8c">
docs/gettingStarted/install.rst
</a>
</li>
<li class="file-stats">
<a href="#f6fd38662d0696a7f4554040b8fec01f4f63546b">
docs/gettingStarted/quickStart.rst
</a>
</li>
<li class="file-stats">
<a href="#32be2c2e3690a70b96e3263f2bb4aa0ce226602a">
docs/running/cliOptions.rst
</a>
</li>
<li class="file-stats">
<a href="#8e4430ed91538c989bbba29d0f6541cce24a88d1">
docs/running/cloud/amazon.rst
</a>
</li>
<li class="file-stats">
<a href="#040bb5962a87ee2772d8d1741c810c1727cf0bcc">
docs/running/cloud/azure.rst
</a>
</li>
<li class="file-stats">
<a href="#9d336859ebc50ce12f946e32de94343f00be9ebb">
docs/running/cloud/clusterUtils.rst
</a>
</li>
<li class="file-stats">
<a href="#2a53c4a04324247c2fb07f240c51435da9975175">
docs/running/cloud/gce.rst
</a>
</li>
<li class="file-stats">
<a href="#54aa56c0c0e2cd49ea7a6083879baecb55a418b1">
docs/running/cwl.rst
</a>
</li>
<li class="file-stats">
<a href="#23df65cbc06731222c916cd45cb6b24f00c5460e">
docs/running/hpcEnvironments.rst
</a>
</li>
</ul>
<h5>The diff was not included because it is too large.</h5>
</div>
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