Clarity edit.
Clarity edit.
Fix for finding RNA-SeQC .jar file.
Added rna-seqc to the test configuration file.
whitespace fixes
Added provenance tracking.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added htseq-count to output files named as the sample name.
Merge branch 'htseq-fix-wip'
Put htseq-count files into their own directory.
Concatenate variant files split by regions using a simplified approach that avoids GATK overhead and file locking issues. Requires sorting files by region then simple concat in order
Additional updates to in-development installation process: Bug fixes, better progress reporting and write output system YAML files
Additional work to finalize new installation and upgrade approach: pointer to new minicona, minimum installation support and documentation start
Ensure good helper messages when no parameters specified for bcbio_nextgen
Use bamtools for merging BAM files, avoding need for batching seen with Picard approach. Do not use out_file for single sample merges. Provides back-compatibility with previous naming change: https://github.com/chapmanb/bcbio-nextgen/commit/ea571e0a60d349c96cb5e7e0c479079383cc6c71
Ensure local parallel runs work with new IPython global setup
Expanding config variables such as  and , module system specific
Typo on gatk
Merge pull request #61 from brainstorm/master

Expanding config variables such as $GATK_PATH and $PICARD_DIR, module system specific
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen