Add function to generalize biotype lookup.

Look in either the source column or in the gene_biotype info
field for protein_coding, if it is in either one, then use that
as the biotype column.

Also fix for replacing rnaseq directory with a link
if a directory already exists

Thanks to @zeneofa for the bug report.
Add vardict as default install target for bcbio. (chapmanb/bcbio-nextgen#514)
Move to bcbio.variation v0.1.7 (chapmanb/bcbio-nextgen#513)
Update Arabidopsis and C elegans support to recent versions: TAIR10 and WBcel235
Update to latest RNA-seq annotations from @roryk (chapmanb/bcbio-nextgen#504)
add qsignature

add download qsignature data

add download qsignature data 2

add download qsignature data 3
Merge pull request #180 from lpantano/upstream

add qsignature
Install oncofuse.
Update homebrew manifest to avoid using deprecated 'brew which' command. Ensure cmake gets updated as dependency to other tools
Merge branch 'master' of https://github.com/chapmanb/cloudbiolinux into nmdp-ngs-pipeline