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