as far as I know the GATK wrappers > 3.4 are community maintained, there
is not much we can do for you here.
I personally stopped to work on GATK because of the license issues and
all I know is that the iuc/devteam datamanager worked for GATK2.8.
Am 01.03.2016 um 13:52 schrieb Scott Szakonyi:
Sorry to be repetitive, but this issue is really blocking our efforts to
develop the workflow that we need in our instance of Galaxy. If anyone
has any familiarity with the issue described below, please let me know.
I really need to get this solved.
One of my co-administrators is having some issues with data
indexed/processed with data managers in GATK. His email to me:
Currently there is no way to load a genome into versions of GATK
above version 1.4. No version seems to be able to load a reference
from history and only version 1.4 seems to work with the available
picard-gatk data manager. We need to be able to work with these
later versions of GATK, 3.4 on the Galaxy tool shed is the latest.
Scott B. Szakonyi
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
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