[med-svn] [Git][med-team/toil][master] 13 commits: skip galaxy-lib, not yet packaged for Debian

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
ee60b837 by Michael R. Crusoe at 2019-01-07T10:04:13Z
skip galaxy-lib, not yet packaged for Debian

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6302fee8 by Michael R. Crusoe at 2019-01-07T10:31:40Z
fix doc build

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1f2f49b3 by Michael R. Crusoe at 2019-01-07T10:47:12Z
Adjust docs for a Debian installed Toil.

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cf924632 by Michael R. Crusoe at 2019-01-07T10:52:51Z
more missing deps

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46d02fb7 by Michael R. Crusoe at 2019-01-07T10:54:53Z
New upstream version 3.18.0
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6d56cbba by Michael R. Crusoe at 2019-01-07T10:55:03Z
Update upstream source from tag 'upstream/3.18.0'

Update to upstream version '3.18.0'
with Debian dir edf8f711b582380aed6ca6f96befa1ceeb8b18e2
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1689c770 by Michael R. Crusoe at 2019-01-07T11:07:34Z
Update patches for 3.18.0

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32dd207a by Michael R. Crusoe at 2019-01-07T11:13:01Z
try building for Python 3

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1e5a132b by Michael R. Crusoe at 2019-01-07T11:19:07Z
cgcloud is no longer needed (moved into Toil itself).

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009d8c47 by Michael R. Crusoe at 2019-01-07T12:22:12Z
adjust to newer cwltool

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37d9aed9 by Michael R. Crusoe at 2019-01-07T12:26:17Z
Don't ship cwltoil, use toil-cwl-runner instead.

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cd3bade7 by Michael R. Crusoe at 2019-01-07T12:35:12Z
better document the patches

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dc9c6567 by Michael R. Crusoe at 2019-01-07T12:46:10Z
Fix spelling.

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30 changed files:

- .gitignore
- Makefile
- README.rst
- attic/toil-sort-example.py
- debian/changelog
- debian/clean
- debian/control
- + debian/patches/adjust_to_newer_cwltool
- + debian/patches/debianize_docs
- + debian/patches/no_galaxy_lib
- debian/patches/no_virtualenv_to_create_manpages.patch
- debian/patches/series
- debian/patches/setting_version.patch
- + debian/patches/spelling
- debian/patches/version.patch
- debian/rules
- docs/appendices/environment_vars.rst
- docs/contributing/contributing.rst
- docs/developingWorkflows/developing.rst
- docs/developingWorkflows/toilAPIBatchsystem.rst
- docs/developingWorkflows/toilAPIFilestore.rst
- docs/gettingStarted/install.rst
- docs/gettingStarted/quickStart.rst
- docs/running/cliOptions.rst
- docs/running/cloud/amazon.rst
- docs/running/cloud/azure.rst
- docs/running/cloud/clusterUtils.rst
- docs/running/cloud/gce.rst
- docs/running/cwl.rst
- docs/running/hpcEnvironments.rst


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/toil/compare/faad0bfc68d9b1c0e1ac367172561f3c90474760...dc9c65671624eef6b331259c906cf34714492a5f

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View it on GitLab: https://salsa.debian.org/med-team/toil/compare/faad0bfc68d9b1c0e1ac367172561f3c90474760...dc9c65671624eef6b331259c906cf34714492a5f
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