changeset 6:88a4d4c31bb6

Deleted selected files
author saket-choudhary
date Thu, 20 Jun 2013 14:04:59 -0400
parents 5417d7cb27a0
children 168b9ff24bcb
files README panama.xml panama_run.py test-data/PANAMA_results.csv test-data/sim_expr.csv test-data/sim_snps.csv tool_dependencies.xml
diffstat 7 files changed, 0 insertions(+), 1742 deletions(-) [+]
line wrap: on
line diff
--- a/README	Thu Jun 20 18:27:53 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-This is a wrapper for a set of eQTL analysis tools.
-
-Though, currently only PANAMA is supported. 
-PANAMA takes in input as :
-
-$panama expression_data.csv snp_data.csv
-
-Where expression_data.csv is a Comma Separated Values file containing the gene expression data 
-in the following format:
-
-         sample1, sample2, ..., sampleN
-  gene1  value ,  value , ...,  value
-  gene2  value ,  value , ...,  value
-  ...
-  geneN
-
-and snp_data.csv contains the SNP data encoded as [0,1,2] in the following format:
-
-        sample1, sample2, ..., sampleN
-  SNP1  value ,  value , ...,  value
-  SNP2  value ,  value , ...,  value
-  ...
-  SNPQ
-
-Make sure panama is installed and available on your path for all nodes.
-Move the test-data files to your galaxy root test-data folder and
-create a directory galaxy-central/tools/eqtl_tools and put
-the panama_run.py and panama.xml files inside eqtl_tools directory.
--- a/panama.xml	Thu Jun 20 18:27:53 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<tool id="panama1" name="panama"  version="1.0.0">
-    <requirements>
-        <requirement type="package" version="0.4">panama</requirement>
-    </requirements>
-    <description>eQTL Analysis using PANAMA(http://ml.sheffield.ac.uk/qtl/panama/)</description>
-    <command interpreter="python">
-        panama_run.py --exp_data=$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>
--- a/panama_run.py	Thu Jun 20 18:27:53 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__()
--- a/test-data/PANAMA_results.csv	Thu Jun 20 18:27:53 2013 +0530
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,401 +0,0 @@
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