This issue was corrected yesterday in change sets
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 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>
> 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
> 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:
> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: