I have a new instance of galaxy cloudman running and have added tools from the toolshed to it. When I attempt to run tools like sam-to-bam or any gatk tool I am prompted for a reference genome. However, indices/references not available for these tools. I have added the following line to the sam_fa_indices.loc, but that did nothing:
index hg19 /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/gh19.fa
I have also added the following three lines to the gatk2_picard_index.loc:
hg19 hg19 Human (hg19) /mnt/galaxyIndices/genomes/Hsapiens/hg19/seq/hg19.fa
GRCh37 GRCh37 Human (GRCh37) /mnt/galaxyIndices/genomes/Hsapiens/GRCh37/seq/GRCh37.fa
mm10 mm10 Mouse (mm10) /mnt/galaxyIndices/genomes/Mmusculus/mm10/seq/mm10.fa
I know I have missed something, but can't seem to figure it out. Could someone point me in the right direction?
Iry T. Witham
Scientific Applications Administrator
Computational Sciences Group
The Jackson Laboratory
600 Main Street
Bar Harbor, ME 04609
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