Andreas Kuntzagk wrote:
I'm definitely pro adding this to galaxy.
I found a minor problem: the line job = model.Job.get ( job_wrapper.job_id )
gave me an error. (type object 'Job' has no attribute 'get') But since I don't want the username as jobname I just commented it out.
In upgrading to SQLAlchemy 0.5, we removed the name mapping. This can be rewritten as: job = self.sa_session.query( self.app.model.Job ).get( job_wrapper.job_id )
Before adding it to galaxy main I'd suggest reworking the parameter-part of the URL. It looks ugly and confusing as it is. (but I cant come up with something better ATM :-( )
This is our hesitation as well, but we've come up with an idea that we hope is cleaner: define them as requirements in tool_conf.xml, like so: <tool file="filters/headWrapper.xml"> <runner name="GalaxyProject"> <requests virtual_free="7G"/> <parallel_environment>threads 4</parallel_environment> </runner> </tool> Where 'GalaxyProject' is a 4-field runner URL as described by Assaf. --nate