Mercurial > repos > trinity_ctat > align_and_estimate_abundance

comparison trinityToolWrapper.py @ 7:78d12a725443 draft

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Adding additional requirements for align_and_estimate_abundance.
author trinity_ctat
date Tue, 26 Sep 2017 14:31:27 -0400
parents 12bc09b4a26d
children 28f6d3b8e931
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6:12bc09b4a26d 7:78d12a725443
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: 47 else:
48 print "Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH." 48 sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, or ensure that directory is in the PATH before running.")
49 sys.exit()
50
49 51
50 # get bindir 52 # get bindir
51 bindir = sys.argv[0] 53 bindir = sys.argv[0]
52 bindir = bindir.split("/") 54 bindir = bindir.split("/")
53 if len(bindir) > 1: 55 if len(bindir) > 1: