Mercurial > repos > peterjc > mira4_assembler

comparison tools/mira4_0/mira4_bait.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
17 """Run MIRA to find its version number""" 17 """Run MIRA to find its version number"""
18 # At the commend line I would use: mira -v | head -n 1 18 # At the commend line I would use: mira -v | head -n 1
19 # however there is some pipe error when doing that here. 19 # however there is some pipe error when doing that here.
20 cmd = [mira_binary, "-v"] 20 cmd = [mira_binary, "-v"]
21 try: 21 try:
22 child = subprocess.Popen(cmd, 22 child = subprocess.Popen(cmd, universal_newlines=True,
23 stdout=subprocess.PIPE, 23 stdout=subprocess.PIPE,
24 stderr=subprocess.STDOUT) 24 stderr=subprocess.STDOUT)
25 except Exception as err: 25 except Exception as err:
26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) 26 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
27 sys.exit(1) 27 sys.exit(1)
86 cmd = " ".join(cmd_list) 86 cmd = " ".join(cmd_list)
87 # print cmd 87 # print cmd
88 start_time = time.time() 88 start_time = time.time()
89 try: 89 try:
90 # Run MIRA 90 # Run MIRA
91 child = subprocess.Popen(cmd_list, 91 child = subprocess.Popen(cmd_list, universal_newlines=True,
92 stdout=subprocess.PIPE, 92 stdout=subprocess.PIPE,
93 stderr=subprocess.STDOUT) 93 stderr=subprocess.STDOUT)
94 except Exception as err: 94 except Exception as err:
95 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err)) 95 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
96 sys.exit(1) 96 sys.exit(1)