Mercurial > repos > mini > strelka
changeset 14:ca84a74ff567
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(-) [+] |
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--- 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" />