version 0.1 of copycat in pipeline
removed unneeded option
adding dump-bins option, removing defunct normal-samtools option
Merge branch 'master' into copycat
Merge branch 'master' into copycat
copycat testing code
adding gc option for testing
Merge branch 'master' into copycat
adding custom entrypoint option, removing default
fixing compire error
Updated genemark to work after new version installed
fix for module definition
Add options for allpaths
Merge branch 'updated2' into gb_master
BladeRunner is not used for anything.