--- a/panama_run.py	Fri Jun 21 10:56:27 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,71 +0,0 @@
-#!/usr/bin/env python
-"""
-Run panama on expression and snp data
-usage: panama_run.py [options]
-   --exp_data: Expression data CSV file
-   --snp_data: SNP data file
-   --output1: Output CSV dataset
-"""
-
-import optparse, os, sys, subprocess, tempfile, shutil
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.cookbook import doc_optparse
-from galaxy import util
-
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-
-
-def __main__():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '', '--exp_data', dest='exp_data', help='The input Expression dataset')
-    parser.add_option( '', '--snp_data', dest='snp_data', help='The input snp dataset' )
-    parser.add_option( '', '--output1', dest='output1', help='The output CSV dataset' )
-    ( options, args ) = parser.parse_args()
-
-    try:
-        tmp_dir = tempfile.mkdtemp()
-        panama_output_file_name = os.path.join(tmp_dir, "PANAMA_results.csv")
-        command = 'panama %s %s -d %s' %(options.exp_data,options.snp_data,tmp_dir)
-        print command
-        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-        tmp_stderr = open( tmp, 'wb' )
-        proc = subprocess.Popen( args=command, shell=True, stderr=tmp_stderr.fileno() )
-        returncode = proc.wait()
-        tmp_stderr.close()
-        # get stderr, allowing for case where it's very large
-        tmp_stderr = open( tmp, 'rb' )
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += tmp_stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        tmp_stderr.close()
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        #clean up temp files
-        print e
-        if os.path.exists( tmp_dir ):
-            shutil.rmtree( tmp_dir )
-        stop_err( 'Error opening panama')
-    # Move tmp_aligns_file_name to our output dataset location
-    shutil.move( panama_output_file_name, options.output1 )
-    #clean up temp files
-    if os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
-    # check that there are results in the output file
-    if os.path.getsize( options.output1 ) > 0:
-        sys.stdout.write( 'PANAM results generated' )
-    else:
-        stop_err( 'Error generating PANAMA results' )
-
-if __name__=="__main__": __main__()