Package the tool. Support gatk4 from conda. Add --genome option. #12
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1. The tools can be installed with `./setup.py install`/`./setup.py develop`, or uploaded into PyPI repository to be installed with pip. Corresponding code changes: - rename "modules" to "conpair" to avoid clashes with other libs on system - import module files instead of sourcing with imp - add setup.py - move common functions to conpair/__init__.py - .gitignore eggs/dist/build 2. If `gatk` executable is available in PATH, the tool will assume it's GATK4 and use it directly (unless --gatk or $GATK_JAR set). It allows to use GATK4 from bioconda. 3. GRCh37 is assumed by default, however if you want to run against GRCh38 or mouse genome, you can specify genome build name with `-g`/`--genome` option (as an alternative to referencing the markers file directly with `--markers`)
…mples out into the root folder. Add pip and conda install docs. CONPAIR_DIR env var is not needed
(it prints lines without the 5th column in the pileup output)
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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
gatkexecutable is available inPATH, the tool will assume it's GATK4 and use it directly (unless--gatkor $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/--genomeoption (as an alternative to referencing the markers file directly with--markers).