I've installed the latest version (using GATK2.8-1) of the GATK2 wrapper here.
I've run into the following error:
##### ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-V7IrBw) does
I see via much googling that this error is due to a user input problem. I've
tried pointing the gatk2_picard_index.loc file in tool-data to the proper data
hg19 hg19 hg19 /software/packages/galaxy/data/picard/hg19.fa
where the following files exist:
I'm using a torque setup. A bam file is being used as input. After much trial
and error I've been unable to figure out what I'm missing.
None of the solutions on google apply to my situation.
Has anyone else run into this configuration problem and solved it?
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS B3H 3Z1
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