Name: Trinity_CTAT_galaxy
Owner: National Cancer Informatics Program
Description: Files needed for Galaxy tools used to run Trinity_CTAT workflows.
Created: 2015-02-20 20:54:28.0
Updated: 2016-10-24 17:41:00.0
Pushed: 2017-04-13 13:24:37.0
Homepage: null
Size: 1374
Language: JavaScript
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|---|---|
| Timothy Tickle | 2015-11-26 05:23:15.0 | 5 |
| Carrie | 2016-09-07 20:54:50.0 | 54 |
| Brian Haas | 2015-05-21 13:39:01.0 | 15 |
Other Committers
| User | Most Recent Commit | # Commits | |
|---|---|---|---|
| Asma Bankapur | bankapur@delanatii.broadinstitute.org | 2016-09-03 03:35:29.0 | 13 |
| Asma Bankapur | bankapur@kcodevel.broadinstitute.org | 2015-11-13 01:29:06.0 | 15 |
| kcopipe | kcopipe@delanatii.broadinstitute.org | 2016-06-21 23:00:29.0 | 5 |
| kcopipe | kcopipe@kcodevel.broadinstitute.org | 2016-04-23 15:23:55.0 | 4 |
Files needed for Galaxy tools used to run Trinity_CTAT workflows.
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
MUTATION_RESOURCES - contains jar files for mutation as well as Hg19 fasta, bed and star indices; required vcf files and cravat files.
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 = ''