diff gaussian.py @ 2:ed472dc06c20 draft default tip

Uploaded 1.0.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaussian.py	Tue Sep 18 23:03:01 2012 -0400
@@ -0,0 +1,54 @@
+#/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)