Hello Geert,

This issue was corrected yesterday in change sets 
https://bitbucket.org/galaxy/galaxy-central/commits/96fdb9168f28b2ffa463195d084c9278efb2465a
 and 
https://bitbucket.org/galaxy/galaxy-central/commits/58a057a02b896ae6d32571f7141f46ccb9006e54,
 which are currently available in both the default and stable branches  of the 
galaxy-central repository.  The fix will be automatically pushed to the 
galaxy-dist repository at some point, but I'm not sure when - I believe it will 
be some time today.

If you are tracking the stable branch on the galaxy-central repository, you can:

hg pull
hg update stable

If you are tracking the galaxy-dist repository, you can get the fix later today.

Thanks for reporting this, and sorry for the inconvenience.

Greg Von Kuster

On Jun 4, 2014, at 6:25 AM, Geert Vandeweyer <geert.vandewey...@uantwerpen.be> 
wrote:

> Hi, 
> 
> I installed the GATK2 wrapper from iuc on the lastest galaxy version. It 
> fails to create the GATK2_PATH and GATK2_SITE_OPTIONS structures under the 
> /tool_dependency_dir/environment_settings/ location, without a clear error 
> (says 'never installed'). 
> 
> If I create the files manually, I can see them through : Admin - Manage 
> installed toolshed repos - gatk2 - missing tool dependencies - GATK2_PATH
> If I click the hyperlink for GATK2_PATH here (this is the install missing 
> dependency page), I can expand and show the GATK2_PATH / env.sh file 
> 
> <ghfbhgbd.png>
> 
> Still, running GATK2 tools (eg UG, gives me in the logs: 
> galaxy.jobs.handler INFO 2014-06-04 12:18:07,333 (78998) Job dispatched
> galaxy.tools.deps WARNING 2014-06-04 12:18:07,928 Failed to resolve 
> dependency on 'gatk2', ignoring
> galaxy.tools.deps WARNING 2014-06-04 12:18:07,971 Failed to resolve 
> dependency on 'GATK2_PATH', ignoring
> galaxy.tools.deps WARNING 2014-06-04 12:18:07,974 Failed to resolve 
> dependency on 'GATK2_SITE_OPTIONS', ignoring
> 
> and tool error: 
> Unable to access jarfile /GenomeAnalysisTK.jar
> 
> For my mutect_wrapper in test.toolshed, which I initially copied from the 
> gatk2 wrapper, the exact same setup seems to work. 
> 
> Any help would be appreciated. 
> 
> Best, 
> 
> Geert
> -- 
> 
> 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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