Back on the topic again, I found another real issue with toolshed tools. I can
configure the toolshed tool to be used by drmaa in universe_wsgi.ini, then
restart Galaxy and everything's good. However, if I modify the tool .xml file
and reload it using the Admin link, it goes back to the defaul
OK, forget what I said earlier. I was watching for a different toolshed tool
than what I reconfigured. Never mind, using the guid (the long tool_id shown
as an example below) worked correctly. The job was pushed out to the cluster
and finished normally.
Sorry about the fuss.
David
On Jul 2
Hi David,
If using the actual tool id (guid) does not work, then it's likely that the job
runner code needs to be fixed to correctly handle tools installed from a tool
shed. I've created a ticket to get this resolved which you can follow so that
you'll receive status changes on the issue.
htt
I found the guid for the tool and tried the usual method of configuring
galaxy to use it via drmaa. With your example, it would be
toolshed.g2.bx.psu.edu/repos/devteam/freebayes/freebayes/0.0.2 =
drmaa://-l nodes=1/
But this didn't have any effect. It still ran on the localhost. I guess
no one
Hi David,
I'm not familiar enough with the job runners to know what the problem may be,
However, for tools installed from the tool shed, the tool id is the tool-shed
generated "guid" instead of the "id" attribute value of the tool config's
tag. So, for example, if you install the freebayes t
Is there a way to configure a tool downloaded from the toolshed depot to use a
job runner other than the local runner? The tool_id for the toolshed tool
isn't honored in universe_wsgi.ini the way the default tools are.
Specifically, has anyone configured a toolshed tool to use drmaa instead of
