Provide a way to check MuTect's version. However due to an issue,
it reports the GATK version it is based on instead: until this is
fixed, we use a hack knowing that 1.1.4 is based on GATK 2.2 and
1.1.5 on GATK 2.7.
Ensure that only MuTect 1.1.5 or higher is allowed to run
Remove hack for MuTect errors, not needed anymore with 1.1.5
Only use cached MuTect version
Use LooseVersion from distutils to ensure a better version check
Merge pull request #106 from mariogiov/master

Bugfix for bowtie2 call in bcbio.pipeline.alignment
Merge pull request #104 from lbeltrame/mutect-version-fix

Ensure only MuTect 1.1.5+ is used when doing tumor analysis
Ensure mutect version always returned when cached (#104). Add Mario to contributors
Switch to samtools cat for BAM merging, working around issues with bamtools requirement for open file handles
Automatically write bcbio-nextgen version during install, including git revision if a development version. Report version and hash in provenance/programs for full tracking to exact revisions. Fixes #39
Update tarball for test genomes to include refFlat version of transcripts. Fixes #107
Capture version information on third party software and libraries used during RNA-seq pipeline
Move essential version check to initial pipeline startup to catch older versions earlier. Identifies samtools version errors before problems during alignment or BAM merging
Added rnaseqc to the default system configuration.
Improve speed in checking bamprep samples during re-runs with many regions
Merge pull request #10 from chapmanb/master

Merge from Brad upstream
Removing unneeded config changes in post_process-sample.yaml
Merge branch 'master' into kalkyl_test_config
Support for TopHat 2.0.9: handle extra paired end output with single-mate matching secondary results. Filter these prior to continuing the pipeline. Thanks to @mariogiov for report
Merge pull request #11 from chapmanb/master

Support for TopHat 2.0.9: handle extra paired end output with single-mat...