shutil
Merge remote-tracking branch 'upstream/master'
get changes in setup_genome
fix setup_genome
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
fix error when restart rnaseq and cufflinks is already done
add kraken
Merge branch 'master' of https://github.com/lpantano/bcbio-nextgen
add kraken to QC summary
add some exception in case kraken DB is not given, and add kraken to bcbio_system
add kraken db installation
update branch
merge with brad's branch
Merge remote-tracking branch 'remotes/upstream/master'
Merge remote-tracking branch 'origin'
Correctly summarize ensemble structural variant calls when calls not found within size range. Thanks to @kspham for test data. Fixes #685. Fixes #687
fix merging fastqs when only 1 file in the list
change qsnp memory limit