# HG changeset patch
# User malex
# Date 1348023717 14400
# Node ID 28ebcfcb10a2d816469300ced2adbb01d3f18e5d
# Parent  33301cfd5fb1d09abbb27787ce06529c1f90fb1f
Deleted to remove the extra folder level.

diff -r 33301cfd5fb1 -r 28ebcfcb10a2 gaussian/gaussian.py
--- a/gaussian/gaussian.py	Tue Sep 18 23:00:40 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-#/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)
diff -r 33301cfd5fb1 -r 28ebcfcb10a2 gaussian/gaussian.xml
--- a/gaussian/gaussian.xml	Tue Sep 18 23:00:40 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<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>
diff -r 33301cfd5fb1 -r 28ebcfcb10a2 gaussian/gaussian_datatype.xml
--- a/gaussian/gaussian_datatype.xml	Tue Sep 18 23:00:40 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-<datatype extension="com" type="galaxy.datatypes.data:Text" subclass="True" display_in_upload="true"/>
diff -r 33301cfd5fb1 -r 28ebcfcb10a2 gaussian/gaussian_job_rules.py
--- a/gaussian/gaussian_job_rules.py	Tue Sep 18 23:00:40 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-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