Commit 65ff36dd authored by Adam Caprez's avatar Adam Caprez
Browse files

Change to have Pegasus handle the http download

parent 4b245b7d
......@@ -250,17 +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 file we create the download job
# and output file. Base output files will be
# 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"])
output_file = File(output_name)
self.files[output_name] = output_file
job = Job(self.executables["download_fastq.py"])
job.uses(output_file, link=Link.OUTPUT, transfer=True)
job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["md5sum"])
self.jobs[output_name] = job
self.dax.addJob(job)
self._add_file(output_name,"http://" + f["url"],"local")
return
def _add_align(self):
......
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