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<mailto:dan@bx.psu.edu>> Date: Thursday, October 2, 2014 1:57 PM To: Iry Witham <iry.witham@jax.org<mailto:iry.witham@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.Witham@jax.org<mailto: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<x-msg://12/iry.witham@jax.org> <372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3].png> The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.