comparison trinityToolWrapper.py @ 2:9e5c3f162eca draft

Needed to dereference links when searching for TRINITY_BASE_DIR.

1:b33e9252e6b4

TRINITY_BASE_DIR = ""
if os.environ.has_key('TRINITY_HOME'):
    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
else:
    # Cicada Dennis added looking for the location of the Trinity program using the unix "which" utility.
    # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
    try:
        pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
    except:
        t, v, tb = sys.exc_info()
        sys.stderr.write("You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running this");
        raise t, v, tb
    else:
        output1, err1 = pipe1.communicate()
        # Take off the last part of the path (which is the Trinity command)
        TRINITY_BASE_DIR = "/".join(output1.split("/")[0:-1])

# get bindir
bindir = sys.argv[0]
bindir = bindir.split("/")
if len(bindir) > 1:

2:9e5c3f162eca

TRINITY_BASE_DIR = ""
if os.environ.has_key('TRINITY_HOME'):
    TRINITY_BASE_DIR = os.environ['TRINITY_HOME'];
else:
    # 2017-09-26
    # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility.
    # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that.
    # I just found distutils.spawn.find_executable() which might work, but already implemented the below.
    try:
        pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE)
    except:
        t, v, tb = sys.exc_info()
        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]);
        raise t, v, tb
    else:
        TrinityPath, err_info = pipe1.communicate()
        # FIX - probably should be checking err_info for errors...
        # Determine the TRINITY_BASE_DIR from output1.
        # If TrinityPath is a link, we need to dereference the link.
        while os.path.islink(TrinityPath)
            TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath))
        # Take off the last part of the path (which is the Trinity command)
        TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1])

# get bindir
bindir = sys.argv[0]
bindir = bindir.split("/")
if len(bindir) > 1: