Add Genome reference in rna-pipeline
Adding RNAQC script. Not finished!
Download RNA-SeQC as a part of the setup
Move RNAQC to qscript dir
Removed remenant Broad qscripts
Refactoring extensions package
More refactoring of the extensions package
Extension for RNASeQC
Added missing project_id argument
Adding RNAQC to rna-pipeline
Corect output paths for RNA-QC
Actually passing rRNA scripts
Adding file name as note
Request 3 cores (and 12 GB RAM) for aligmentQC
Added travis yml for CI
Adding install command
Trying to get travis to run setup
Change run tests to false.

Since the tests carry so many external dependencies I changed them to not run as default. Running them will have to be done manually at a resourse where all external programs, e.g. bwa, etc. have been setup.
Extracting reader API
The first commit of the New Illumina report reader