Commit 58d4d879 authored by Adam Caprez's avatar Adam Caprez
Browse files

Merge branch 'master' of git.unl.edu:aknecht2/chipathlon

Conflicts:
	chipathlon/workflow_job.py
parents 5f168016 5ed3105e
......@@ -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)
......
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