Mercurial > repos > malex > gaussian

--- /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 <zhang@hpc.ufl.edu> and Oleksandr Moskalenko <om@hpc.ufl.edu>
+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)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaussian.xml	Tue Sep 18 23:03:01 2012 -0400
@@ -0,0 +1,52 @@
+<tool id="gaussian" name="Gaussian" version="1.0.0">
+<!--
+Copyright (C) 2012
+Ying Zhang <zhang@hpc.ufl.edu> and Oleksandr Moskalenko <om@hpc.ufl.edu>
+University of Florida Research Computing
+-->
+  <description>Computational Chemistry software for electronic structure modeling.</description>
+  <command interpreter="python">gaussian.py $__user_name__ $infile</command>
+  <inputs>
+        <param format="txt" name="infile" type="data" label="Gaussian Input File"/>
+  </inputs>
+  <outputs>
+        <data format="txt" name="outfile" type="data" from_work_dir="gaussian.log" label="${tool.name} on ${on_string}: Output" />
+  </outputs>
+  <!--
+  <stdio>
+        <exit_code range="1:"   level="fatal"   description="Tool Error - see debug log." />
+        <exit_code range="2:"   level="fatal"   description="Unauthorized user - see help." />
+  </stdio>
+  -->
+  <tests>
+    <test>
+      <param name="infile" value="chemistry/gaussian/gaussian.com"/>
+      <output name="outfile" file="chemistry/gaussian/gaussian.log"/>
+    </test>
+</tests>
+
+  <help>
+**Gaussian version g09**
+
+Gaussian is Electronic Structure Modeling Software. It has license restrictions.
+To run it you must sign the Gaussian Confidentiality Agreement. The agreement
+form is available in NPB 2238 during normal business hours.
+
+
+Running Gaussian from Galaxy is currently in testing stage. Please report any
+problems to the `UF HPC Support &lt;http://support.hpc.ufl.edu&gt;`_.
+
+
+Batch job resource request can be specified at the beginning of the input file
+as in the following example:
+
+&#37;nproc=8 - number of cores (ppn).
+
+&#37;mem=2000mb - memory size (pmem) can be set in kb, mb, gb, kw, mw, or gw. Words are used as the default.
+
+!walltime=12:00:00 - run time (walltime) in HH:MM:SS format.
+
+
+Detailed information on program usage is available from `the Gaussian website &lt;http://www.gaussian.com/&gt;`_.
+  </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaussian_datatype.xml	Tue Sep 18 23:03:01 2012 -0400
@@ -0,0 +1,1 @@
+<datatype extension="com" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="true"/>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gaussian_job_rules.py	Tue Sep 18 23:03:01 2012 -0400
@@ -0,0 +1,54 @@
+def gaussian(job):
+    inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
+    inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
+    src_comfile = inp_data[ "infile" ].file_name
+    comfile = open(src_comfile, 'r')
+    ppn='1'
+    pmem = '900mb'
+    overhead = 200
+    walltime = '11:59:59'
+    for line in comfile:
+        line = line.strip().lower()
+        if ( "%nproc=" in line):
+            try:
+                ppn = line.split('=')[1]
+            except Exception, e:
+                log.debug(e)
+                sys.stdout.write(e)
+        if ("%mem=" in line):
+            try:
+                mem_str = line.split('=')[1]
+                if ( "kb" in mem_str ):
+                    mem_num = mem_str.split('kb')[0]
+                    mem_num = int(int(mem_num) / 1024.0) + overhead
+                if ( "mb" in mem_str ):
+                    mem_num = mem_str.split('mb')[0]
+                    mem_num = int(mem_num) + overhead
+                elif ( "gb" in mem_str ):
+                    mem_num = mem_str.split('gb')[0]
+                    mem_num = (int(mem_num) * 1024) + overhead
+                elif ( "kw" in mem_str ):
+                    mem_num = mem_str.split('kw')[0]
+                    mem_num = int(int(mem_num) * 8 / 1024.0) + overhead
+                elif ( "mw" in mem_str ):
+                    mem_num = mem_str.split('mw')[0]
+                    mem_num = (int(mem_num) * 8) + overhead
+                elif ( "gw" in mem_str ):
+                    mem_num = mem_str.split('gw')[0]
+                    mem_num = (int(mem_num) * 8 * 1024) + overhead
+                else:
+                    #Assume words
+                    mem_num = int(int(mem_str) * 8 / 1024.0 / 1024.0) + overhead
+                pmem_num = int(mem_num / int(ppn))
+                pmem = str(pmem_num) + 'mb'
+            except Exception, e:
+                log.debug(e)
+                sys.stdout.write(e)
+        if ("!walltime=" in line):
+            try:
+                walltime = line.split('=')[1]
+            except Exception, e:
+                log.debug(e)
+                sys.stdout.write(e)
+    request = "-l nodes=1:ppn=%s,pmem=%s,walltime=%s" % (ppn, pmem, walltime)
+    return 'drmaa://%s/' % request