Mercurial > repos > trinity_ctat > align_and_estimate_abundance

comparison trinityToolWrapper.py @ 9:b6152cc26ffd draft

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Trying to fix a syntax error.
author trinity_ctat
date Tue, 26 Sep 2017 15:14:48 -0400
parents 28f6d3b8e931
children a8fa525a2f30
comparison
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8:28f6d3b8e931 9:b6152cc26ffd
24 try: 24 try:
25 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) 25 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
26 except: 26 except:
27 msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0]) 27 msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0])
28 sys.stderr.write(msg) 28 sys.stderr.write(msg)
29 t, v, tb = sys.exc_info() 29 # t, v, tb = sys.exc_info()
30 raise t, v, tb 30 # raise t, v, tb
31 # For some reason the above was giving a syntax error.
32 # A simple raise shoudl reraise the existing exception.
33 raise
31 else: 34 else:
32 TrinityPath, err_info = pipe1.communicate() 35 TrinityPath, err_info = pipe1.communicate()
33 # FIX - probably should be checking err_info for errors... 36 # FIX - probably should be checking err_info for errors...
34 # Determine the TRINITY_BASE_DIR from output1. 37 # Determine the TRINITY_BASE_DIR from output1.
35 # If TrinityPath is a link, we need to dereference the link. 38 # If TrinityPath is a link, we need to dereference the link.