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.vandewey...@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I found the following trello card, but its a little bit outdated: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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--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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