Hi Team,

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)    
GRCh37  GRCh37  Human (GRCh37)  
mm10    mm10    Mouse (mm10)    

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
Phone: 207-288-6744
email: iry.wit...@jax.org


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