Hi Jim,

latest changes here:
https://bitbucket.org/BjoernGruening/gatk2

- more use of macros
- new tool_dependencies that just sets the GATK2_PATH and
GATK2_SITE_OPTIONS
- added GALAXY_SLOTS to all tools
- changes some inconsistency in loc file naming

> 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.  

Ok, I added a few of these parameters and will hopefully find some
testers in the next weeks.

> 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.  

-nc is now a macro
-nct is hardcoded in 5 tools and they all have a different value

> 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! I don't mind, as you like. If you have time to integrate
patches, we can go with your repository. I personally prefer git, but I
can use that without problems. As you like :) 
Do you think we should create an IUC repository for GATK2? 
Do you know how the plans are for GATK2 inside of Galaxy main? I would
like to keep duplication at a minimum.

@Geert:
-et is now configurable with a ENV variable in the installed env.sh file
(default is 'not set') and max_jvm_heap_fraction is deactivated by
default.
 
Ciao,
Bjoern


> 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
> > > > > > 
> > > > > > ___________________________________________________________
> > > > > > Please keep all replies on the list by using "reply all"
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> > > > > > 
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> > > >         
> > > 
> > 
> > 

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