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 <dan@bx.psu.edu>
Date: Thursday, October 2, 2014 1:57 PM
To: Iry Witham <iry.witham@jax.org>
Cc: "galaxy-dev@lists.bx.psu.edu" <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.Witham@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.witham@jax.org


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