Hello Geert, This issue was corrected yesterday in change sets https://bitbucket.org/galaxy/galaxy-central/commits/96fdb9168f28b2ffa463195d... and https://bitbucket.org/galaxy/galaxy-central/commits/58a057a02b896ae6d32571f7..., 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.vandeweyer2@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.vandeweyer@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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