[med-svn] [Git][med-team/paleomix][master] 6 commits: New upstream version 1.2.13.2

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / paleomix


Commits:
b69c70cd by Andreas Tille at 2018-05-03T12:13:41+02:00
New upstream version 1.2.13.2
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d62f69e3 by Andreas Tille at 2018-05-03T12:13:55+02:00
Update upstream source from tag 'upstream/1.2.13.2'

Update to upstream version '1.2.13.2'
with Debian dir 6b1ec91029816a90c53862c3a1e13cda5b68d8d3
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cdb551f5 by Andreas Tille at 2018-05-03T12:13:55+02:00
New upstream version

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1d7d7f2b by Andreas Tille at 2018-05-03T12:15:50+02:00
Point Vcs fields to salsa.debian.org

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ca90f19c by Andreas Tille at 2018-05-03T12:15:50+02:00
Standards-Version: 4.1.4

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fa31afcf by Andreas Tille at 2018-05-03T13:17:16+02:00
For some reason the -Xmx argument will be dropped when constructing  the java call.  Just drop it from the test as well.

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30 changed files:

- CHANGES.md
- MANIFEST.in
- README.rst
- bin/bam_pipeline
- bin/bam_rmdup_collapsed
- bin/conv_gtf_to_bed
- bin/paleomix
- bin/phylo_pipeline
- bin/trim_pipeline
- debian/changelog
- debian/control
- + debian/patches/adapt_java_calling_test.patch
- debian/patches/avoid_downloading_prerequisites.patch
- debian/patches/series
- docs/bam_pipeline/filestructure.rst
- docs/conf.py
- docs/index.rst
- misc/setup_bam_pipeline_example.sh
- misc/setup_phylo_pipeline_example.sh
- misc/skeleton.py
- misc/synthesize_reads.py
- paleomix/__init__.py
- paleomix/atomiccmd/__init__.py
- paleomix/atomiccmd/builder.py
- paleomix/atomiccmd/command.py
- paleomix/atomiccmd/pprint.py
- paleomix/atomiccmd/sets.py
- paleomix/common/__init__.py
- paleomix/common/bamfiles.py
- paleomix/common/bedtools.py


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/paleomix/compare/d308f95884314f4218040f89700f490c8551b7a5...fa31afcf165faf4970941e0487f37c905d636b39

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View it on GitLab: https://salsa.debian.org/med-team/paleomix/compare/d308f95884314f4218040f89700f490c8551b7a5...fa31afcf165faf4970941e0487f37c905d636b39
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