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<mailto:afg...@gmail.com>>
Date: Saturday, October 4, 2014 6:10 AM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@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,
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<mailto: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<mailto:d...@bx.psu.edu>>
Date: Thursday, October 2, 2014 1:57 PM
To: Iry Witham <iry.wit...@jax.org<mailto:iry.wit...@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.wit...@jax.org<mailto: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<tel:207-288-6744>
email: iry.wit...@jax.org


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