CHANGES.md

 # 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

+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@debian.org>  Wed, 11 Sep 2019 11:21:12 +0200
+
 paleomix (1.2.13.3-1) unstable; urgency=medium
 
   * New upstream version

debian/compat

-11

debian/control

@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@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.