Hi Gordon, That's very useful. I have particularly been after a way to alter the SGE parameters on a tool by tool basis as clearly an NGS alignment tool requires many more resources than a 'cut'. Our galaxy server is just for internal use (currently), so the username may not be as useful. I'll have a go at implementing it. Cheers, Chris Assaf Gordon wrote:
Hello,
I'm trying to move our Galaxy to the our SGE cluster, and I need couple of fine-tuning tweaks.
1. set a project name (in addition to the queue) - globally, and per tool. 2. set extra QSUB options per tool 3. Specify the actual user who submitted the job - in the "email" field and as the job name.
Details: The project name is needed for accounting (requested by our SGE admins).
To specify a project name, add a fourth slash to the sge URL in universe_wsgi.ini, as so: --- ## Global SGE project name , for all tools default_cluster_job_runner = sge:////GalaxyProject/
## Tool specific project name Cut1 = sge:////OtherGalaxyProject/ ----
The extra QSUB options per tool allow requesting nodes with more memory or request more cores (=threads) per job. To specify extra options, add a fifth slash to the sge tool runner URL in univer_wsge.ini, as so: ---- ## Tool specific parameters - ## run 'cut' on a node with at least 7GB of ram Cut1 = sge:////GalaxyProject/-l virtual_free=7G/
## run 'select first lines' on a node with 4 cores, and reserve all the cores for the tool ## allowing multi-threaded 'select lines' operation ;) Show beginning1 = sge:////GalaxyProject/-R y -pe threads 4/ ---- Note: specifying extra parameters ALWAYS overrides the project name (but the project name can be an empty string).
The actual user is needed to quickly see (with qstat) who runs what (currently, the job names are "galaxy_NNNN.sh").
Comments are welcomed, -gordon.