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comparison trinityToolWrapper.py @ 2:9e5c3f162eca draft

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Needed to dereference links when searching for TRINITY_BASE_DIR.
author trinity_ctat
date Tue, 26 Sep 2017 11:34:17 -0400
parents a9723c18d389
children 32b6a47c9312
comparison
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1:b33e9252e6b4 2:9e5c3f162eca
15 15
16 TRINITY_BASE_DIR = "" 16 TRINITY_BASE_DIR = ""
17 if os.environ.has_key('TRINITY_HOME'): 17 if os.environ.has_key('TRINITY_HOME'):
18 TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; 18 TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
19 else: 19 else:
20 # Cicada Dennis added looking for the location of the Trinity program using the unix "which" utility. 20 # 2017-09-26
21 # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
21 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. 22 # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
23 # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
22 try: 24 try:
23 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) 25 pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
24 except: 26 except:
25 t, v, tb = sys.exc_info() 27 t, v, tb = sys.exc_info()
26 sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running this"); 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]);
27 raise t, v, tb 29 raise t, v, tb
28 else: 30 else:
29 output1, err1 = pipe1.communicate() 31 TrinityPath, err_info = pipe1.communicate()
32 # FIX - probably should be checking err_info for errors...
33 # Determine the TRINITY_BASE_DIR from output1.
34 # If TrinityPath is a link, we need to dereference the link.
35 while os.path.islink(TrinityPath)
36 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
30 # Take off the last part of the path (which is the Trinity command) 37 # Take off the last part of the path (which is the Trinity command)
31 TRINITY_BASE_DIR = "/".join(output1.split("/")[0:-1]) 38 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
32 39
33 # get bindir 40 # get bindir
34 bindir = sys.argv[0] 41 bindir = sys.argv[0]
35 bindir = bindir.split("/") 42 bindir = bindir.split("/")
36 if len(bindir) > 1: 43 if len(bindir) > 1: