Mercurial > repos > trinity_ctat > align_and_estimate_abundance

comparison trinityToolWrapper.py @ 3:32b6a47c9312 draft

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Fix python syntax error.
author trinity_ctat
date Tue, 26 Sep 2017 11:43:35 -0400
parents 9e5c3f162eca
children cb71c6b0bf66
comparison
equal deleted inserted replaced
2:9e5c3f162eca 3:32b6a47c9312
23 # I just found distutils.spawn.find_executable() which might work, but already implemented the below. 23 # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
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 t, v, tb = sys.exc_info() 27 t, v, tb = sys.exc_info()
28 sys.stderr.write("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("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.".format(sys.argv[0]))
29 raise t, v, tb 29 raise t, v, tb
30 else: 30 else:
31 TrinityPath, err_info = pipe1.communicate() 31 TrinityPath, err_info = pipe1.communicate()
32 # FIX - probably should be checking err_info for errors... 32 # FIX - probably should be checking err_info for errors...
33 # Determine the TRINITY_BASE_DIR from output1. 33 # Determine the TRINITY_BASE_DIR from output1.