On Nov 5, 2012, at 2:15 PM, Carlos Borroto carlos.borroto@gmail.com wrote:
On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko om@hpc.ufl.edu wrote:
Here is the blastn rule procedure code and the relevant snippet of the default runner procedure. I just added the database based multiplier, so this part is very simple at the moment. I just set a bogus multiplier of "4" for the "nt_*" databases as an example.
Hi Alex,
This is great and definitely helped me get going!. I found a few issues related to my local configuration. Like I'm using ncbi_blastn_wrapper that was migrated to the tool_shed, so I had to use: elif 'ncbi_tblastn_wrapper' in tool_id_src
Instead of: elif tool_id_src.startswith('ncbi_blastn_wrapper'):
The id for the tool from the shed_tool is: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.0.13
Hopefully this won't break later on.
I hear you. I though of using regexes to avoid that sort of breakage, but instead started using the output of "tool_id_src = tool_id.split("/")[-2]" for my startswith matches. It works well enough.
I also need to go back a do a better configuration of our local grid engine( using SGE ), as I did only a very bare bone installation and I'm running into this error: DeniedByDrmException: code 17: unknown resource "nodes"
Which I realize is a configuration issue in my SGE.
Right, my code is Torque/MOAB specific. You need to rewrite the resource requests to use "pe", "slots", "h_vmem", and "h_rt" instead depending on your GE setup. It's an easy change.
Last, and this was my mistake. I didn't initially realize that this example you share here, assumes all tools will call default_runner(), which in turn will call an specific function to figure out the drmaa options to set. I was trying to use the lines from your previous email: ncbi_blastn_wrapper = dynamic:///python/ncbi_blastn ncbi_blastp_wrapper = dynamic:///python/ncbi_blastp
Yes, I switched from using separate runner lines to routing the jobs from the default runner as a more flexible approach.
But note to myself and anybody else following the thread, the function being called from universe_wsgi.ini needs to return a proper drmaa/pbs url.
Thanks again!, Carlos
Also, the newest error handling code depends on the changeset John put up in a merge request into galaxy-central.
Regards,
Alex