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comparison trinityToolWrapper.py @ 6:12bc09b4a26d draft

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Adding TrinityPath/util to the PATH so other utilities can be found.
author trinity_ctat
date Tue, 26 Sep 2017 13:58:08 -0400
parents 98d99fed9d35
children 78d12a725443
comparison
equal deleted inserted replaced
5:98d99fed9d35 6:12bc09b4a26d
42 print "That path is a link." 42 print "That path is a link."
43 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) 43 TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
44 print "The new path is: {:s}".format(TrinityPath) 44 print "The new path is: {:s}".format(TrinityPath)
45 # Take off the last part of the path (which is the Trinity command) 45 # Take off the last part of the path (which is the Trinity command)
46 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) 46 TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])
47 else:
48 print "Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH."
47 49
48 # get bindir 50 # get bindir
49 bindir = sys.argv[0] 51 bindir = sys.argv[0]
50 bindir = bindir.split("/") 52 bindir = bindir.split("/")
51 if len(bindir) > 1: 53 if len(bindir) > 1:
54 else: 56 else:
55 bindir = "." 57 bindir = "."
56 58
57 59
58 ## add locations of tools to path setting. 60 ## add locations of tools to path setting.
59 TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt"; 61 #TOOL_PATHS_FILE = bindir + "/__add_to_PATH_setting.txt";
60 for line in open(TOOL_PATHS_FILE): 62 #for line in open(TOOL_PATHS_FILE):
61 line = line.rstrip() 63 # line = line.rstrip()
62 os.environ['PATH'] += ":" + line 64 # os.environ['PATH'] += ":" + line
65
66 # Add TrinityPath and its utils to the PATH environment variable.
67 # print "Initially the PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
68 os.environ['PATH'] = os.environ['PATH'] + ":{:s}:{:s}".format(TRINITY_BASE_DIR,TRINITY_BASE_DIR+"/util")
69 # print "Now the PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
63 70
64 71
65 def stop_err( msg ): 72 def stop_err( msg ):
66 sys.stderr.write( "%s\n" % msg ) 73 sys.stderr.write( "%s\n" % msg )
67 sys.exit() 74 sys.exit()
77 84
78 # If one needs to silence stdout 85 # If one needs to silence stdout
79 #args.append( ">" ) 86 #args.append( ">" )
80 #args.append( "/dev/null" ) 87 #args.append( "/dev/null" )
81 print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR) 88 print "The TRINITY_BASE_DIR is:\n\t{:s}".format(TRINITY_BASE_DIR)
89 print "The PATH env variable is:\n\t{:s}".format(os.environ['PATH'])
82 90
83 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]); 91 args[0] = "".join([TRINITY_BASE_DIR, '/', args[0]]);
84 92
85 cmdline = " ".join(args) 93 cmdline = " ".join(args)
86 94