Hi Iry,
Yeah, I see what you mean about that *env.sh* file not being in the GATK2
repo the readme states so. I'm not sure what's exactly supposed to be in
that file for GATK2 in particular so perhaps one of the wrapper authors can
jump in. For majority of tools, you'd just need something like this in
there: 
*PATH=/mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/bin:$PATH
<http://toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/bin:$PATH>*
and
have placed the binaries for the tool in that directory.

If nobody else jumps in, I'll poke around more in the coming days.

On Tue, Oct 7, 2014 at 11:58 AM, Iry Witham <iry.wit...@jax.org> wrote:

>  Hi Enis,
>
>  Thanks for that information.  Now I am getting an error with the
> Unified_Genotyper failing to locate the GenomeAnalysisTK.jar.  I discovered
> that gatk2 needs to be downloaded and installed.  I have done that, but
> can't seem to figure out where the env.sh file reference below exists.  Can
> you point me to the correct proximity of that file?  Or do I need to create
> the file and if so where?
>
>  Thanks,
> Iry
>
>     Galaxy wrapper for GATK2
>
> This wrapper is copyright 2013 by Björn Grüning, Jim Johnson & the Galaxy
> Team.
>
> The Genome Analysis Toolkit or GATK is a software package developed at the
> Broad Institute to analyse next-generation resequencing data. The toolkit
> offers a wide variety of tools, with a primary focus on variant discovery
> and genotyping as well as strong emphasis on data quality assurance. Its
> robust architecture, powerful processing engine and high-performance
> computing features make it capable of taking on projects of any size.
>
> http://www.broadinstitute.org/gatk
> http://www.broadinstitute.org/gatk/about/citing-gatk
>
> GATK is Free for academics, and fee for commercial use. Please study the
> GATK licensing website:
> http://www.broadinstitute.org/gatk/about/#licensing
>   Installation
>
> The recommended installation is by means of the toolshed
> <http://toolshed.g2.bx.psu.edu/view/iuc/gatk2>.
>
> Galaxy should be able to install samtools dependencies automatically for
> you. GATK2, and its new licence model, does not allow us to distribute the
> GATK binaries. As a consequence you need to install GATK2 by your own,
> please see the GATK website for more information:
>
> http://www.broadinstitute.org/gatk/download
>
> Once you have installed GATK2, you need to edit the env.sh files that are
> installed together with the wrappers. You must edit the GATK2_PATH
> environment variable in the file:
>
>
> <tool_dependency_dir>/environment_settings/GATK2_PATH/iuc/gatk2/<hash_string>/env.sh
>
> to point to the folder where you have installed GATK2.
>
> Optionally, you may also want to edit the GATK2_SITE_OPTIONS environment
> variable in the file:
>
>
> <tool_dependency_dir>/environment_settings/GATK2_SITE_OPTIONS/iuc/gatk2/<hash_string>/env.sh
>
> to deactivate the 'call home feature' of GATK with something like:
>
> GATK2_SITE_OPTIONS='-et NO_ET -K /data/gatk2_key_file'
>
> GATK2_SITE_OPTIONS can be also used to insert other specific options into
> every GATK2 wrapper at runtime, without changing the actual wrapper.
>
> Read more about the "Phone Home" problem at:
> http://www.broadinstitute.org/gatk/guide/article?id=1250
>
> Optionally, you may also want to add some commands to be executed before
> GATK (e.g. to load modules) to the file:
>
> <tool_dependency_dir>/gatk2/default/env.sh
>
> Finally, you should fill in additional information about your genomes and
> annotations in the gatk2_picard_index.loc and gatk2_annotations.txt. You
> can find them in the tool-data/ Galaxy directory.
>
>   From: Enis Afgan <afg...@gmail.com>
> Date: Saturday, October 4, 2014 6:10 AM
>
> 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,
> 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>
>>
>>   The information in this email, including attachments, may be
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>>
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>> you received this email by mistake, please notify the sender by return
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>>
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>
>   The information in this email, including attachments, may be
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