Hi,In my fresh copy of galaxy-dist I am having a problem with tools being run only with the default tool runner and not with the assigned tool runner I created in the [galaxy:tool_runners] section...This is the setting for bwa_wrapper in my universe_wsgi.ini:bwa_wrapper = drmaa://-V -q long.q -pe
Hi, Thon
I'm guessing here: but now that bwa is kept in the toolshed, the tool name
appears to be
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 according
to your job runner entry - so I wonder if that whole ugly string now needs
to be in the tool_runners section to over-ride
Hi Ross,I was indeed expecting something like that and when I tried what you suggestyed, it worked :)you need to use the complete path to the tool (including version number??!?!) in the tool-runner definition to make it be able to be set in the universe_wsgi.ini...So indeed the toolshed move of
On Dec 5, 2012, at 5:10 PM, Anthonius deBoer wrote:
I confirmed that you have to include the version numbers for these toolshed
tools:
This works:
toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/bwa_wrapper/1.2.3 =
drmaa://-V -q long.q -pe smp 4/
this does not:
On Wed, Dec 5, 2012 at 10:56 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Thon,
I just committed a fix for this in 75a97c971d36 that will be available in
our next distribution release. It will also match from most to least
specific so you can define all of:
