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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