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

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.vandeweyer@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer