[med-svn] [Git][med-team/bcbio][master] 9 commits: New upstream version 1.1.3

[Michael R. Crusoe]

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


Commits:
d9e2b213 by Michael R. Crusoe at 2019-02-10T08:40:50Z
New upstream version 1.1.3
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d4433341 by Michael R. Crusoe at 2019-02-10T08:41:40Z
Update upstream source from tag 'upstream/1.1.3'

Update to upstream version '1.1.3'
with Debian dir 66b4b7739104633ad67c5c4511f4d60bbbd50333
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8d2a4655 by Michael R. Crusoe at 2019-02-10T08:42:51Z
new upstream release

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5d78e887 by Michael R. Crusoe at 2019-02-10T08:45:24Z
debian/patches/python3.patch: removed, applied upstream

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b2ff8b83 by Michael R. Crusoe at 2019-02-10T08:55:30Z
add ${sphinxdoc:Built-Using} to -doc

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0b8fbcfe by Michael R. Crusoe at 2019-02-10T09:07:58Z
fixes a few spelling errors

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63353604 by Michael R. Crusoe at 2019-02-10T09:07:58Z
add pytest to enable running the tests

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f188722a by Michael R. Crusoe at 2019-02-10T09:07:59Z
python3-bcbio: section is "python"

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7b98f981 by Michael R. Crusoe at 2019-02-11T07:13:40Z
Add recommendations discovered through testing

and make a list of software that needs packaging

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30 changed files:

- .travis.yml
- HISTORY.md
- bcbio/bam/__init__.py
- bcbio/bam/callable.py
- bcbio/bam/cram.py
- bcbio/bam/fastq.py
- bcbio/broad/__init__.py
- bcbio/cwl/create.py
- bcbio/cwl/cwlutils.py
- bcbio/cwl/defs.py
- bcbio/cwl/hpc.py
- bcbio/cwl/tool.py
- bcbio/cwl/workflow.py
- bcbio/distributed/multi.py
- bcbio/distributed/objectstore.py
- bcbio/distributed/resources.py
- bcbio/distributed/runfn.py
- bcbio/distributed/split.py
- bcbio/galaxy/api.py
- bcbio/galaxy/nglims.py
- bcbio/graph/graph.py
- bcbio/heterogeneity/bubbletree.py
- bcbio/heterogeneity/chromhacks.py
- bcbio/heterogeneity/loh.py
- bcbio/hla/bwakit.py
- bcbio/illumina/flowcell.py
- bcbio/illumina/machine.py
- bcbio/illumina/samplesheet.py
- bcbio/illumina/transfer.py
- bcbio/install.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/5e2407d63b681f9fa7949220147f279132213c62...7b98f981e77e80d109e7b14e4cacc2e544a480a1

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/compare/5e2407d63b681f9fa7949220147f279132213c62...7b98f981e77e80d109e7b14e4cacc2e544a480a1
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