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
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...
Move checks for GATK VariantRecalibrator specific files to immediately before use. Enables standard hard-filtering of non-human organisms during variant calling
Default to solexa-quals if no quality format is provided.
Added note about default quality encoding for Tophat.
Update mm10-resources.yaml
Improve persistence of parameters passed on bcbio_nextgen install and upgrades to facilitate more cusomtized installations
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Provide installation and upgrade options that enable commerical and data-intensive tools. Fixes #111
Avoid using python environmental variables when running bcbio_nextgen.py, avoiding issues where PYTHONHOME or PYTHONPATH point to other library locations
Ensure ensemble variant calls get snpEff annotations for feeding into gemini database
Avoid OS errors due to too long argument lists for samtools merging: create shortened symlinked files to real files and pass those on commandline. Thanks to @brentp for report
Streamline VM creation process on VirtualBox