Package the tool. Support gatk4 from conda. Add --genome option. #12
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Proposing changes that would allow distribution with bioconda and bcbio-nextgen.
./setup.py install
/./setup.py develop
, or uploaded into PyPI repository to be installed with pip. Corresponding code changes:setup.py
,conpair/__init__.py
,If
gatk
executable is available inPATH
, the tool will assume it's GATK4 and use it directly (unless--gatk
or $GATK_JAR are set). It allows to use GATK4 from bioconda. (resolves Support GATK 4 #11).GRCh37 is assumed by default and corresponding markers files are searched, however if the users want to run against GRCh38 or the mouse genome, they can specify genome build name with
-g
/--genome
option (as an alternative to referencing the markers file directly with--markers
).