annotate gaussian.py @ 2:ed472dc06c20 draft default tip

Uploaded 1.0.0

#/usr/bin/env python
"""
Copyright (C) 2012
Ying Zhang <[e-mail]> and Oleksandr Moskalenko <[e-mail]>
University of Florida Research Computing

This script checks the user permission for using gaussian software.
If permission is granted, it runs g09 with inputfile.

It takes 2 command line options:
    $name: the $__user_name__ template preset that corresponds to the real
username.
    $inputfile: a input file for g09
"""
import sys, os, shutil
from subprocess import Popen, PIPE

if len(sys.argv) == 3:
    name = sys.argv[1]
    ginput = sys.argv[2]
else:
    msg = "Error: wrong number of parameters provided.\n"
    sys.stderr.write(msg)
    sys.exit(1)

command = "groups " + name + " | grep gaussian"
result = Popen([command], shell=True, stdout=PIPE, stderr=PIPE, close_fds=True)
stdout, stderr = result.communicate()
return_code = result.returncode
if return_code:
    errmsg = "Error: only users in the gaussian group can use this software.\n"
    sys.stdout.write(stdout)
    sys.stderr.write(errmsg)
    sys.stderr.write(stderr)
    sys.stderr.write("Return error code %i from command:\n" % return_code)
    sys.stderr.write("%s\n" % command)
    sys.exit(2)
else:
    if not os.path.exists('gaussian.com'):
        shutil.copyfile(ginput, 'gaussian.com')
    cmd = 'source /galaxy/run/dev/tools/chemistry/env.sh; g09 gaussian.com'
    result = Popen([cmd], shell=True, stdout=PIPE, stderr=PIPE, close_fds=True)
    stdout, stderr = result.communicate()
    return_code = result.returncode
    if return_code:
        sys.stdout.write(stdout)
        sys.stderr.write(stderr)
        sys.stderr.write("Return error code %i from command:\n" % return_code)
        sys.stderr.write("%s\n" % result)
        sys.exit(1)
    else:
        sys.stdout.write(stdout)
        sys.stdout.write(stderr)
        sys.exit(0)