comparison strelka_wrapper.py @ 14:ca84a74ff567

corriging bug in environment variable

12:3421b0fbec61

#For Geviteam 2014

"""
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
from string import Template
from galaxy import eggs

            #need to index this bam file
            command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename )
            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 )
    parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )   
    parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False )

    analysis_dir=job_dir + "/StrelkaAnalysis"
    config_script=root_dir + "/configureStrelkaWorkflow.pl"
    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)


    #verifying eveything's ok
    if not os.path.isfile(config_script):
    	sys.exit("ERROR: The strelka workflow must be built prior to running. See installation instructions in '$root_dir/README'")

    print("**** starting workflow.")
    print("**** workflow cmd: '" + cmd + "'")
    my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
    print("**** completed workflow execution")

14:ca84a74ff567

#For Geviteam 2014

"""
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
from string import Template
from galaxy import eggs

            #need to index this bam file
            command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename )
            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 )
    parser.add_argument( '-n', '--normalBam', help='path to tumor bam file', required = False )   
    parser.add_argument( '-r', '--refFile', help='path to tumor bam file', required = False )

    analysis_dir=job_dir + "/StrelkaAnalysis"
    config_script=root_dir + "/configureStrelkaWorkflow.pl"
    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)


    #verifying eveything's ok
    if not os.path.isfile(config_script):
    	sys.exit("ERROR: The strelka workflow must be built prior to running. See installation instructions in '$root_dir/README'")

    print("**** starting workflow.")
    print("**** workflow cmd: '" + cmd + "'")
    my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
    print("**** completed workflow execution")

if __name__=='__main__':
    __main__()