Warning
This repository has been archived and is no longer maintained.
The code is provided for historical reference and may contain unpatched or unknown vulnerabilities.
It should not be used in production systems.
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.