# HG changeset patch
# User Saket Choudhary <saketkc@gmail.com>
# Date 1373360626 -19800
# Node ID 1a89e2bd4a9210be7a550340bf9d988949fe80f3
# Parent  b63c04e54c008299b79e24f5c3b0ee252ea38ca1
Fix organisation

diff -r b63c04e54c00 -r 1a89e2bd4a92 panama.xml
--- a/panama.xml	Tue Jul 09 04:56:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<tool id="panama1" name="panama"  version="1.0.0">
-    <requirements>
-        <requirement type="package" version="0.4">panama</requirement>
-    </requirements>
-    <description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description>
-    <command interpreter="python">
-        panama_run.py --exp_data=$expression_data --snp_data=$snp_data --output1=$output1
-    </command>
-    <inputs>
-        <param name="expression_data" type="data" format="text" label="Select Expression Data" />
-        <param name="snp_data" type="data" format="text" label="Select SNP data" />
-    </inputs>
-    <outputs>
-        <data name="output1" format="text" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="expression_data" value="sim_expr.csv" />
-            <param name="snp_data" value="sim_snps.csv" />
-            <output name="output1" file="PANAMA_results.csv" />
-        </test>
-    </tests>
-
-
-</tool>
diff -r b63c04e54c00 -r 1a89e2bd4a92 panama_run.py
--- a/panama_run.py	Tue Jul 09 04:56:18 2013 -0400
+++ /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__()
diff -r b63c04e54c00 -r 1a89e2bd4a92 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Jul 09 04:56:18 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,15 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="panama" version="0.4">
-        <install version="1.0">
-            <actions>
-                <action type="setup_virtualenv">panama</action>
-            </actions>
-        </install>
-        <readme> PANAMA installation needs numpy ,scipy, matplotlib, ipython, cython, pandas, pygp.
-            Please change the "backend" to "Agg" as "backend: Agg"  </readme>
-    </package>
-</tool_dependency>
-
-
-
diff -r b63c04e54c00 -r 1a89e2bd4a92 tools/eqtl_tools/panama.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/eqtl_tools/panama.xml	Tue Jul 09 14:33:46 2013 +0530
@@ -0,0 +1,25 @@
+<tool id="panama1" name="panama"  version="1.0.0">
+    <requirements>
+        <requirement type="package" version="0.4">panama</requirement>
+    </requirements>
+    <description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description>
+    <command interpreter="python">
+        panama_run.py --exp_data=$expression_data --snp_data=$snp_data --output1=$output1
+    </command>
+    <inputs>
+        <param name="expression_data" type="data" format="text" label="Select Expression Data" />
+        <param name="snp_data" type="data" format="text" label="Select SNP data" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="text" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="expression_data" value="sim_expr.csv" />
+            <param name="snp_data" value="sim_snps.csv" />
+            <output name="output1" file="PANAMA_results.csv" />
+        </test>
+    </tests>
+
+
+</tool>
diff -r b63c04e54c00 -r 1a89e2bd4a92 tools/eqtl_tools/panama_run.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/eqtl_tools/panama_run.py	Tue Jul 09 14:33:46 2013 +0530
@@ -0,0 +1,71 @@
+#!/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__()
diff -r b63c04e54c00 -r 1a89e2bd4a92 tools/tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/tool_dependencies.xml	Tue Jul 09 14:33:46 2013 +0530
@@ -0,0 +1,15 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="panama" version="0.4">
+        <install version="1.0">
+            <actions>
+                <action type="setup_virtualenv">panama</action>
+            </actions>
+        </install>
+        <readme> PANAMA installation needs numpy ,scipy, matplotlib, ipython, cython, pandas, pygp.
+            Please change the "backend" to "Agg" as "backend: Agg"  </readme>
+    </package>
+</tool_dependency>
+
+
+