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.




Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be

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