Thanks Jim,

I cloned it under:
https://bitbucket.org/BjoernGruening/gatk2

and added macros. 

If you agree I will try to do the following during the next week:

- add GALAXY_SLOTS 
--------------------
--num_threads | -nt will be \${GALAXY_SLOTS:-4} and 
-nct / --num_cpu_threads_per_data_thread will be set to a fixed value
according to
http://www.broadinstitute.org/gatk/guide/tagged?tag=multithreading

- adding new features if necessary
- Adopting the tool_dependencies.xml
- Adopting the readme file

Help and suggestions would be appreciated.
Thanks!
Bjoern


> 
> 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.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
> > > > 
> > > > ___________________________________________________________
> > > > Please keep all replies on the list by using "reply all"
> > > > in your mail client.  To manage your subscriptions to this
> > > > and other Galaxy lists, please use the interface at:
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> > > > 
> > > > To search Galaxy mailing lists use the unified search at:
> > > >    http://galaxyproject.org/search/mailinglists/
> > > 
> >     
> > 
> 
> 
> -- 
> James E. Johnson, Minnesota Supercomputing Institute, University of
> Minnesota 



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