Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_convert.py @ 34:0785a6537f3e draft

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planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 6405ba93fcec7ea93452bf54d559c7507ee7a57c
author peterjc
date Wed, 07 Jun 2017 12:33:39 -0400
parents 56b421d59805
children 259891fce7fd
comparison
equal deleted inserted replaced
33:1291ed21789f 34:0785a6537f3e
27 27
28 def run(cmd): 28 def run(cmd):
29 # Avoid using shell=True when we call subprocess to ensure if the Python 29 # Avoid using shell=True when we call subprocess to ensure if the Python
30 # script is killed, so too is the child process. 30 # script is killed, so too is the child process.
31 try: 31 try:
32 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) 32 child = subprocess.Popen(cmd, universal_newlines=True,
33 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
33 except Exception as err: 34 except Exception as err:
34 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) 35 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
35 # Use .communicate as can get deadlocks with .wait(), 36 # Use .communicate as can get deadlocks with .wait(),
36 stdout, stderr = child.communicate() 37 stdout, stderr = child.communicate()
37 return_code = child.returncode 38 return_code = child.returncode