Commit 85ee93ae authored by aknecht2's avatar aknecht2
Browse files

Fixed minor spacing issues in workflow. Added profiles for jobtime and memory into workflow_ob.

parent 72808100
......@@ -250,10 +250,10 @@ class Workflow(object):
if exp_name not in self.files and control_name not in self.files:
run["input_sets"].append(pair)
for f in pair:
# For each fastq, have Pegasus do the http fetching.
# Files are named EXPID_ACCESSION.fastq.gz
# For each fastq, have Pegasus do the http fetching.
# Files are named EXPID_ACCESSION.fastq.gz
output_name = "%s_%s.fastq.gz" % (run["experiment"], f["accession"])
self._add_file(output_name,"http://" + f["url"],"dummylocal")
self._add_file(output_name, "http://" + f["url"], "dummylocal")
return
def _add_align(self):
......@@ -307,7 +307,7 @@ class Workflow(object):
pegasus.catalog.site.file = %s/sites.xml
pegasus.condor.logs.symlink = false
pegasus.transfer.links=true
pegasus.transfer.links=true
pegasus.data.configuration = sharedfs
""" % (os.path.join(self.basepath, "input"),))
wh.write(pegasusrc)
......
......@@ -111,7 +111,9 @@ class WorkflowJob(object):
for f in output_files:
job.uses(f["file"], link=Link.OUTPUT, transfer=True)
job.addArguments(*self._create_arg_list(input_files, output_files))
## ADd memory / walltime
# Add memory / walltime
job.profile(Namespace.GLOBUS, "maxwalltime", self.params["walltime"] if "walltime" in self.params else self.base[self.jobname]["walltime"])
job.profile(Namespace.GLOBUS, "maxmemory", self.params["memory"] if "memory" in self.params else self.base[self.jobname]["walltime"])
return job
else:
print self.err
......
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