On Nov 5, 2012, at 2:15 PM, Carlos Borroto <carlos.borr...@gmail.com> wrote:
> On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko <o...@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
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