Commit 5ed3105e authored by aknecht2's avatar aknecht2
Browse files

Revert "Fixed minor spacing issues in workflow. Added profiles for jobtime...

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

This reverts commit 85ee93ae.
parent 107edb5f
......@@ -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)
......
......@@ -111,9 +111,7 @@ 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
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"])
## ADd memory / walltime
return job
else:
print self.err
......
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