It looks like I need to generate the dict file for the mm10 reference as well 
as add the reference to the srma_index.loc.  My question is where do these need 
to exist?  Do they belong in the repo directory structure or or in the primary 
tool-data directory?  The hg19.fa, hg19.fa.fia, hg19.dict as well as these same 
files for the mm9 GRCh37. However, the .dict does not exist for mm10.  Even 
though that is the case the references do not appear in the gatk2 tools.

Any ideas?

Thanks,
Iry

From: Daniel Blankenberg <d...@bx.psu.edu<mailto:d...@bx.psu.edu>>
Date: Thursday, October 2, 2014 1:57 PM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@jax.org>>
Cc: "galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>" 
<galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: Re: [galaxy-dev] Cloudman indices installation/configuration

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<mailto: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<x-msg://12/iry.wit...@jax.org>


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