Hi Dan,

Thanks for pointing out the tab issue.  However, I have made the modification 
and restarted my instance, but still get no reference genome listed.  It is 
funny that there are a limited number of tools that have this issue.  They are:

SAM Tools:
Generate pileup
SAM-to-BAM
Mpileup
SNP/WGA: Data; Filters:
SnpEff
SnpEff Download (cannot select a genome version to download)
NGS: Picard:
SAM/BAM Alignment Summary
SAM/BAM GC Bias
NGS: GATK2 Tools: (All of the tools)

These are tools that I have installed via the toolshed.  Is there a different 
location for the .loc files that need modifying?

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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