Hi Iry,

First thing to check is that your fields are tab delimited — they appear to be 
spaces instead of tabs in this email, but copy and pasting into email can munge 
things sometimes (also “gh19.fa” is probably a typo, but that wouldn’t prevent 
the selection option from showing up).


Thanks for using Galaxy,

Dan


On Oct 2, 2014, at 1:49 PM, Iry Witham <iry.wit...@jax.org> wrote:

> 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)    
> /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?
> 
> Regards,
> __________________________________
> 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
> 
> 
> <372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3].png>
> 
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