Nate Coraor wrote:
Andreas Kuntzagk wrote:
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.
This looks much cleaner. (Moving the runner config to the tool_conf was also somewhere on my wish list.) Only grief I have with this is that you need to have a complete mapping of SGE (or Torque) parameters to XML elements in Galaxy (and in the documentation). Or would you also have something generic like <other_argument>-l my_limit</other_argument> ? regards, Andreas