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.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 I found the following trello card, but its a little bit outdated: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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>
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