Bjoern,

Looks good.

This page also had some info on per tool use of -nt and -nct
  http://www.broadinstitute.org/gatk/guide/tagged?tag=nct

If remember correctly,  GATK doesn't ignore options that don't apply, it just 
does an ungraceful exit.
I not sure if I had that sorted out when I last worked on this.

I'm not sure how much the -nct / --num_cpu_threads_per_data_thread value should 
be tuned,
but it may make sense for that to be a variable or in a macro.

I gave you write permission on: 
http://testtoolshed.g2.bx.psu.edu/view/jjohnson/gatk2
if you care to use that, otherwise we could migrate to a new tool shed 
repository.

Thanks,

JJ



On 11/20/13, 10:19 AM, Bjoern Gruening wrote:
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

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Minnesota




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