Correctly ignore additional custom packages when not specified. Thanks to @roryk
Retrieve VCF index files as part of download to avoid needing to create them. chapmanb/bcbio-nextgen#85
Added the STAR spliced read aligner.
Added RNA-SeQC from the Broad.
Typo fixed.
Merge pull request #96 from roryk/master

Added the STAR spliced read aligner.
Add STAR and rnaseqc to default packages for CloudBioLinux and minimal bcbio-nextgen install
Ubuntu 13.04 work: update STAR aligner to latest alpha release that compiles. Fixes #98. Do not re-install distribute on anaconda systems to avoid bx-python install error. Fixes #97
Update vcftools to the latest version
Added gtfToGenePred to ucsc_tools.
Revert "Added gtfToGenePred to ucsc_tools."

This reverts commit efe9c53057c442533a544d0771cf4252481d9b77.
Fix @roryk commit to add gffToGenePred
Use local build functions for RNA-seq transcript retrieval. Fixes chapmanb/bcbio-nextgen#88
One final fix for local transcript download. Fixes chapmanb/bcbio-nextgen#88
Change source reference in install_venvburrito to dot (they are synonyms in bash, dot available in more shells). Unsure why this is being source'd here (line added in 0567c582f97cc5a70c72cb6fe905f94905b6a4fa by @chapmanb). If the goal was just to activate the burrito, might be better to replace this with env.safe_run('. $HOME/.venvburrito/startup.sh')?