Files needed for Galaxy tools used to run Trinity_CTAT workflows. This repository is the source repository for the user trinity_ctat's tools uploaded to the Galaxy Toolshed.
The following environment variables are needed by various tools in this suite:
FUSION_RESOURCES - contains gencode19 gtf files, bowtie indices, Hg19 fasta and fai files, star indices and gmap indices files for Fusion tools. (Not located in git; do not include in git).
MUTATION_RESOURCES - contains jar files for mutation as well as Hg19 fasta, bed and star indices; required vcf files and cravat files. (Not located in git; do not include in git).
TOOLS - the folder that contains Trinity_CTAT and SciEDPipeR
EXTLIBS - A location that contains external libraries and executables needed for Trinity_CTAT tools to run
TRINTOOLS - usually the same as EXTLIBS, contains the folders DISCASM, STAR-FUSION, FusionInspector, etc
Fusion Inspector Make sure STAR is in your path when using fusion inspector.
SLNCKY In slncky_galaxy_wrapper.py, the following paths will need to be filled in:
BEDTOOLS = ''
LASTZ = ''
LIFTOVER = ''
SCIEDPIPER_HOME = ''
IU specific changes have been saved here; be careful to test your own setup if you use these.