Mercurial > repos > mini > strelka

changeset 14:ca84a74ff567

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corriging bug in environment variable
author mini
date Wed, 01 Oct 2014 12:21:13 +0200
parents 3421b0fbec61
children ae516605f4a5
files strelka.xml strelka_wrapper.py tool_dependencies.xml
diffstat 3 files changed, 6 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/strelka.xml	Tue Sep 30 11:44:07 2014 +0200
+++ b/strelka.xml	Wed Oct 01 12:21:13 2014 +0200
@@ -2,7 +2,7 @@
   <!-- Made by Gregoire Seguin-Henry for geviteam in 2014 -->
   <description>Strelka</description>
   <requirements>
-    <requirement type="set_environment">SCRIPT_PATH</requirement>
+    <requirement type="set_environment">SCRIPT_PATH_STRELKA</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
     <requirement type="package" version="0.1.11">vcftools</requirement>
   </requirements>
--- a/strelka_wrapper.py	Tue Sep 30 11:44:07 2014 +0200
+++ b/strelka_wrapper.py	Wed Oct 01 12:21:13 2014 +0200
@@ -7,7 +7,6 @@
 """
 A wrapper script for running the GenomeAnalysisTK.jar commands.
 """
-
 from __future__ import print_function
 import sys, argparse, os, tempfile, subprocess, shutil
 from binascii import unhexlify
@@ -58,7 +57,6 @@
             my_Popen( command, "fasta_index_stderr", tmp_dir, "Error during indexation of fasta file :" + fasta_filename)
 
 def __main__():
-
     #Manage options
     parser = argparse.ArgumentParser()                                             
     parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False )
@@ -96,7 +94,7 @@
     tmp_dir = tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' )
     config_ini = "%s/config.ini" % (tmp_dir)
 
-    #print("root_dir: " + root_dir + "\njob_dir :" + job_dir + "\nanalysis_dir :" + analysis_dir + "\nconfig_script :" + config_script + "\ntmp_dir :" + tmp_dir + "\nconfig_ini :" +  config_ini)
+    print("root_dir: " + root_dir + "\njob_dir :" + job_dir + "\nanalysis_dir :" + analysis_dir + "\nconfig_script :" + config_script + "\ntmp_dir :" + tmp_dir + "\nconfig_ini :" +  config_ini)
 
 
     #verifying eveything's ok
@@ -142,3 +140,5 @@
     my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
     print("**** completed workflow execution")
 
+if __name__=='__main__':
+    __main__()
--- a/tool_dependencies.xml	Tue Sep 30 11:44:07 2014 +0200
+++ b/tool_dependencies.xml	Wed Oct 01 12:21:13 2014 +0200
@@ -1,7 +1,7 @@
-<?xml version="1.0"?>
+<?xml version="1.0"?>
 <tool_dependency>
   <set_environment version="1.0">
-     <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
+     <environment_variable name="SCRIPT_PATH_STRELKA" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
   </set_environment>
   <package name="samtools" version="0.1.18">
     <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />