On Wed, Aug 7, 2013 at 3:33 PM, Ganote, Carrie L <cganote@iu.edu> wrote:
Hi John,
That was it. I feel silly. I still have a lot of tooth-cutting to do on python!
I saw the parallel tags in the Blast tool and was very intrigued, but couldn't find reference to it in the read-the-docs or on the Galaxy wiki. Perhaps there is some documentation of this that I missed?
No I don't think there is documentation unless you count the code base the mailing list archive. I think setting use_tasked_jobs to True in universe_wsgi.ini might be all you need to do to start splitting such blast inputs. I think the parallelism tag in the tool file describes how to split the inputs. # This enables splitting of jobs into tasks, if specified by the particular tool config. # This is a new feature and not recommended for production servers yet. #use_tasked_jobs = False I don't use this functionality (at least not in this fashion) so I don't have a lot of advice. Otherwise, if you have a AMQP thing working you should probably just stick with that sounds like a perfectly good way to go. -John
In our case, the python splitting program is doing this: * Take the blast query * Split the sequences up * For each sequence, submit the query and the command to a queue on a RabbitMQ server (Consumers are set up to listen for queries and then run the jobs). * Write each result to a temp file * When all of the sequence jobs are finished, concat the files back in the correct order and write to the output file Galaxy expects
I made a wrapper for this splitter and it works fine on its own. Now I'm trying to add this functionality (run on AMQP) as a user-available option on the Blast tool. So for my dynamic runner, I need to know whether to send the job to DRMAA or to this AMQP python script. Hopefully that makes more sense...
Thanks so much for the help!
-Carrie ________________________________________ From: jmchilton@gmail.com [jmchilton@gmail.com] on behalf of John Chilton [chilton@msi.umn.edu] Sent: Wednesday, August 07, 2013 3:52 PM To: Ganote, Carrie L Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool params passed to python dynamic job runner
I am not sure why the quotations marks are there in the first place, but I do see the problem. replace and strip return new strings, they don't modify the existing variable. This is demonstrated below:
% python
x = ' "Moo Cow" ' x ' "Moo Cow" ' x.replace("\"", "").strip() 'Moo Cow' x ' "Moo Cow" ' x=x.replace("\"", "").strip() x 'Moo Cow'
You will want to change the line:
modulePath.replace("\"", "").strip()
to
modulePath = modulePath.replace("\"", "").strip()
You should also take a look at the Galaxy task splitting framework. It already has the ability to split up blast jobs into multiple tasks. I am not sure the dynamic job runner is what you want for that use case.
-John
On Wed, Aug 7, 2013 at 12:26 PM, Ganote, Carrie L <cganote@iu.edu> wrote:
Hi List,
I've run into a frustration recently with passing values to the dynamic job runner from a tool. Here's what's going on:
in ncbi_blastn_wrapper.xml: <param name="pathToModule" type="hidden" value="/abs/path/to/module" /> ...
in dynamic_runner.py: ... def blastn_wrapper(job): incoming = dict( [ ( p.name, p.value ) for p in job.parameters ] ) modulePath = incoming["pathToModule"] modulePath.replace("\"", "").strip()
dummy = '/abs/path/to/module' equals = (modulePath == dummy) log.debug( '\n~%s~\n~%s~\nsame? %s' % (mypath, dummy, equals) ) ... log: ~"/abs/path/to/module"~ ~/abs/path/to/module~ same? False
I have no idea why these "" are persisting, or if that is even the problem. I can't find the modulePath when using os.path.exists(modulePath). What I want to do is optionally (user checks a box) run another python script that splits up the blast queries into a bunch of jobs and submits each job separately - and I was just going to import this other script using sys.append(modulePath) in some poor attempt to keep the system cleaner.
If this is a problem with my understanding of python, please enlighten me - if there are other tools that pass around paths or if there's another way to do this in less hacky way, I'm open to advice.
Thanks!
Carrie Ganote
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