[med-svn] [Git][med-team/paleomix][master] 7 commits: New upstream version 1.2.13.4
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 11 10:37:29 BST 2019
Andreas Tille pushed to branch master at Debian Med / paleomix
Commits:
95b58c29 by Andreas Tille at 2019-09-11T09:21:12Z
New upstream version 1.2.13.4
- - - - -
30832404 by Andreas Tille at 2019-09-11T09:21:12Z
New upstream version
- - - - -
7358da03 by Andreas Tille at 2019-09-11T09:21:27Z
Update upstream source from tag 'upstream/1.2.13.4'
Update to upstream version '1.2.13.4'
with Debian dir 997dd9406cdcd6f943f8f8d261109b0843150dce
- - - - -
1abc70cd by Andreas Tille at 2019-09-11T09:21:27Z
debhelper-compat 12
- - - - -
347cc6c0 by Andreas Tille at 2019-09-11T09:21:32Z
Standards-Version: 4.4.0
- - - - -
74d07c3b by Andreas Tille at 2019-09-11T09:21:37Z
Use secure URI in Homepage field.
Fixes lintian: homepage-field-uses-insecure-uri
See https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html for more details.
- - - - -
996fb053 by Andreas Tille at 2019-09-11T09:37:11Z
Wait for Python3 port
- - - - -
7 changed files:
- CHANGES.md
- debian/changelog
- − debian/compat
- debian/control
- docs/phylo_pipeline/usage.rst
- paleomix/nodes/picard.py
- paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml
Changes:
=====================================
CHANGES.md
=====================================
@@ -1,5 +1,11 @@
# Changelog
+## [1.2.13.4] - 2019-03-25
+### Fixed
+ - Improved detection of Picard versions in cases where 'java'
+ outputs additional text.
+
+
## [1.2.13.3] - 2018-11-01
### Fixed
- Fixed validation/read counting of pre-trimmed reads not including
@@ -581,7 +587,8 @@ the (partially) updated documentation now hosted on ReadTheDocs.
- Switching to more traditional version-number tracking.
-[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...HEAD
+[Unreleased]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.4...HEAD
+[1.2.13.4]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...v1.2.13.4
[1.2.13.3]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3
[1.2.13.2]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2
[1.2.13.1]: https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+paleomix (1.2.13.4-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * debhelper-compat 12
+ * Standards-Version: 4.4.0
+ * Use secure URI in Homepage field.
+ TODO: see https://github.com/MikkelSchubert/paleomix/issues/15
+
+ -- Andreas Tille <tille at debian.org> Wed, 11 Sep 2019 11:21:12 +0200
+
paleomix (1.2.13.3-1) unstable; urgency=medium
* New upstream version
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
dh-python,
python,
python-setuptools,
@@ -15,10 +15,10 @@ Build-Depends: debhelper (>= 11~),
default-jre-headless,
bowtie2,
rsync
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/paleomix
Vcs-Git: https://salsa.debian.org/med-team/paleomix.git
-Homepage: http://geogenetics.ku.dk/publications/paleomix
+Homepage: https://geogenetics.ku.dk/publications/paleomix
Package: paleomix
Architecture: any
=====================================
docs/phylo_pipeline/usage.rst
=====================================
@@ -22,15 +22,15 @@ To execute the pipeline, a command corresponding to the step to be invoked is us
Samples
-------
-The phylogenetic pipeline expects a number of samples to be specified. Each sample has a name, a gender, and a genotyping method::
+The phylogenetic pipeline expects a number of samples to be specified. Each sample has a name, a sex, and a genotyping method::
Samples:
<GROUP>:
SAMPLE_NAME:
- Gender: ...
+ Sex: ...
Genotyping Method: ...
-Gender is required, and is used to filter SNPs at homozygous sex chromsomes (e.g. chrX and chrY for male humans). Any names may be used, and can simply be set to e.g. 'NA' in case this feature is not used.
+Sex is required, and is used to filter SNPs at homozygous sex chromsomes (e.g. chrX and chrY for male humans). Any names may be used, and can simply be set to e.g. 'NA' in case this feature is not used.
The genotyping method is either "SAMTools" for the default genotyping procedure using samtools mpileupe | bcftools view, or "Random Sampling" to sample one random nucleotide in the pileup at each position. This key may be left out to use the default (SAMTools) method.
=====================================
paleomix/nodes/picard.py
=====================================
@@ -239,7 +239,7 @@ def picard_command(config, command):
requirement = versions.Requirement(call=params.finalized_call,
name="Picard tools",
- search=r"^(\d+)\.(\d+)",
+ search=r"\b(\d+)\.(\d+)\.\d+",
checks=versions.GE(1, 137))
_PICARD_VERSION_CACHE[jar_path] = requirement
=====================================
paleomix/resources/examples/nature_protocols/phylogeny/000_makefile.yaml
=====================================
@@ -8,25 +8,25 @@ Project:
# in 'ExcludeSamples' and 'FilterSingletons'.
Samples:
06_3928A:
- Gender: NA
+ Sex: NA
DDR7602:
- Gender: NA
+ Sex: NA
LBUS5:
- Gender: NA
+ Sex: NA
M-0182896:
- Gender: NA
+ Sex: NA
NL07434:
- Gender: NA
+ Sex: NA
P13527:
- Gender: NA
+ Sex: NA
P13626:
- Gender: NA
+ Sex: NA
P17777:
- Gender: NA
+ Sex: NA
Pi1845A:
- Gender: NA
+ Sex: NA
Pi1889:
- Gender: NA
+ Sex: NA
# Specifies a set of regions of interest, each representing one or more
# named regions in a reference sequence (e.g. genes) in BED format.
View it on GitLab: https://salsa.debian.org/med-team/paleomix/compare/5bd19aa1844a1bd9cb0aa6ce3b92e1bf1a4c40a5...996fb05366794c10bc473f9a0ecce17f822e3fa0
--
View it on GitLab: https://salsa.debian.org/med-team/paleomix/compare/5bd19aa1844a1bd9cb0aa6ce3b92e1bf1a4c40a5...996fb05366794c10bc473f9a0ecce17f822e3fa0
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