I pushed a copy of GATK2 from the testtoolshed to bitbucket:

   https://bitbucket.org/jjohnson/gatk2


The existing tool dependency no longer makes sense with the current licensing and access policies by Broad.  

Also, much of the duplication in the individual tool wrappers could be moved to macros,
as Chilton did in the galaxy-central GATK:   tools/gatk/gatk_macros.xml

Thanks,

JJ


On 11/19/13, 1:28 PM, Björn Grüning wrote:
Hi Geert,

thanks for the information. Are you running GATK-2.4 or GATK-Lite-2.4.
As far I know the lite version is deprecated.

JJ are your wrappers in bitbucket/github? If you agree I would try to
migrate to a recent GATK version and implement GALAXY_SLOTS. Not sure
about the installation recipe ...

Ciao,
Bjoern

Hi,

I have GATK 2.4 running in our local galaxy, next to the default galaxy 
1.x version. Both are in the tool menu, but only users that have 
provided a licence or proof that they are from an academic site have 
access to the 2.4 version. This is based on a usergroup check in a 
dynamic job runner configuration.

I used & modified the GATK 2 tool configuration from the test toolshed 
(by jjohnson). Modifications to the xmls included:
     --max_jvm_heap "xG" instead of --max_jvm_heap_fraction "1"  : we 
use shared nodes, so it's not allowed to use all ram.
     --num_threads  : some hard coded thread settings were changed
     made sure the '--et 'NO_ET' is commented out, as we don't have a key.

relevant dynamic_runner part:

from galaxy.jobs.mapper import JobMappingException
if 'gatk2' in tool_id >= 0:
                         user_group_assocs = user.groups or []
                         user_has_license = 'gatk2_license' in 
[user_group_assoc.group.name for user_group_assoc in user_group_assocs]
                         if not user_has_license:
                                 raise JobMappingException("GATKv2 is 
only available to non-profit, academic users. Please send a mail to 
geert.vandeweyer2@uantwerpen.be to confirm this.")


Best,

Geert


On 11/19/2013 12:26 PM, Bjoern Gruening wrote:
Hi,

I found that the GATK tools do not have the same requirement tag. For
example indel-realigner has version 1.4, realigner_target_creator has
version 1.3. Is that correct? What is the recent version that is
required for GATK?

Also realigner_target_creator uses the "gatk_picard_indexes" location
file, but under tool-data is only a gatk_sorted_picard_indexes.loc
file.

Are there any concrete plans for the GATK wrappers. Especially to update
to a newer version. Or is that not feasible because of this complicated
license policy and the phone-home option ...

I found the following trello card, but its a little bit outdated:
https://trello.com/c/IPkT2spd

Is anyone running a recent GATK version in Galaxy?

Thanks!
Bjoern

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James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota