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.wit...@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 <d...@bx.psu.edu>
> Date: Thursday, October 2, 2014 1:57 PM
> To: Iry Witham <iry.wit...@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.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
>
>
> <372D007A-1B00-4668-BA6B-F0527C1F24BE[34][3].png>
>
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