Hi Iry, Try adding the following to your */mnt/galaxy/galaxy-app/tool_data_table_conf.xml*, populating the referenced files (tool-data/gatk2_picard_index.loc and tool-data/gatk2_annotations.txt) as desired and restarting Galaxy: <!-- Location of Picard dict files valid for GATK --> <table name="gatk2_picard_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> <file path="tool-data/gatk2_picard_index.loc" /> </table> <!-- Available of GATK references --> <table name="gatk2_annotations" comment_char="#"> <columns>value, name, gatk_value, tools_valid_for</columns> <file path="tool-data/gatk2_annotations.txt" /> </table> Hope this gets you going. Let us know if it doesn't, Enis On Fri, Oct 3, 2014 at 1:36 PM, Iry Witham <Iry.Witham@jax.org> wrote:
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 <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
<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.
___________________________________________________________ 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/