--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/strelka_wrapper.py	Fri Sep 26 13:24:13 2014 +0200
@@ -0,0 +1,201 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+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
+#import pkg_resources; pkg_resources.require( "bx-python" )
+
+#GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbSNP', 'picard_interval_list':'interval_list' } #items not listed here will use the galaxy extension as-is
+#GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed
+#DEFAULT_GATK_PREFIX = "gatk_file"
+#CHUNK_SIZE = 2**20 #1mb
+#
+#
+def cleanup_before_exit( tmp_dir ):
+    if tmp_dir and os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+def _create_config(args, config_path):
+    conf_file = open(config_path, "w")
+    conf_file.write("[user]\n")
+    for option in args:
+        if not option in ["tumorBam", "normalBam", "refFile", "configFile"] and args[option]!=None:
+    	    conf_file.write("%s=%s\n" % (option, args[option]))
+    conf_file.close()
+
+def my_Popen(cmd, prefix_for_stderr_name, tmp_dir, msg_error):
+    stderr_name = tempfile.NamedTemporaryFile( prefix = prefix_for_stderr_name ).name
+    proc = subprocess.Popen( args=cmd, shell=True, stderr=open( stderr_name, 'wb' ) )
+    return_code = proc.wait()                          
+    if return_code:
+	for line in open( stderr_name ):
+           print(line, file=sys.stderr)
+	os.unlink( stderr_name ) #clean up
+ 	cleanup_before_exit( tmp_dir )
+ 	raise Exception( msg_error )
+    else:
+        os.unlink( stderr_name )
+
+def index_bam_files( bam_filenames, tmp_dir ):
+    for bam_filename in bam_filenames:
+        bam_index_filename = "%s.bai" % bam_filename
+        print("bam_filename is: " + bam_filename + " bam_index_filename is: " + bam_index_filename + " test is: %s" % os.path.exists(bam_index_filename))
+        if not os.path.exists( bam_index_filename ):
+            #need to index this bam file
+            command = 'samtools index %s %s' % ( bam_filename, bam_index_filename )
+            my_Popen( command, "bam_index_stderr", tmp_dir, "Error during indexation of fasta file :" + bam_filename)
+
+def index_fasta_files( fasta_filenames, tmp_dir ):
+    for fasta_filename in fasta_filenames:
+        fasta_index_filename = "%s.fai" % fasta_filename
+        print("fasta_filename is: " + fasta_filename + " fasta_index_filename is: " + fasta_index_filename + " test is: %s" % os.path.exists(fasta_index_filename))
+        if not os.path.exists( fasta_index_filename ):
+            #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__():
+    #Parse Command Line  OPTPARSE DEPRECIATED USE ARGPARSE INSTEAD
+    #MKTEMP DEPRECIATED USE MKDTlizations#EMP INSTEAD
+        
+    root_dir= "/home/galaxyusr/data/galaxy_dist/tools/strelka2"
+    expected_dir="for_tests"
+    job_dir=os.getcwd()
+    analysis_dir=job_dir + "/StrelkaAnalysis"
+    config_script=root_dir + "/configureStrelkaWorkflow.pl"
+    tmp_dir = "tmp"  #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)
+   
+    #manage parsing
+    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 )
+    parser.add_argument( '-c', '--configFile', help='path to tumor bam file', required = False )
+    parser.add_argument( '--depthFilterMultiple', help='path to tumor bam file', required = False )
+    parser.add_argument( '--snvMaxFilteredBasecallFrac', help='path to tumor bam file', required = False )
+    parser.add_argument( '--snvMaxSpanningDeletionFrac', help='path to tumor bam file', required = False )
+    parser.add_argument( '--indelMaxRefRepeat', help='path to tumor bam file', required = False )
+    parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='path to tumor bam file', required = False )
+    parser.add_argument( '--indelMaxIntHpolLength', help='path to tumor bam file', required = False )
+    parser.add_argument( '--ssnvPrior', help='path to tumor bam file', required = False )
+    parser.add_argument( '--sindelPrior', help='path to tumor bam file', required = False )
+    parser.add_argument( '--ssnvNoise', help='path to tumor bam file', required = False )
+    parser.add_argument( '--sindelNoise', help='path to tumor bam file', required = False )
+    parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='path to tumor bam file', required = False )
+    parser.add_argument( '--minTier1Mapq', help='path to tumor bam file', required = False )
+    parser.add_argument( '--minTier2Mapq', help='path to tumor bam file', required = False )
+    parser.add_argument( '--ssnvQuality_LowerBound', help='path to tumor bam file', required = False )
+    parser.add_argument( '--sindelQuality_LowerBound', help='path to tumor bam file', required = False )
+    parser.add_argument( '--isWriteRealignedBam', help='path to tumor bam file', required = False )
+    parser.add_argument( '--binSize', help='path to tumor bam file', required = False )
+    parser.add_argument( '--extraStrelkaArguments', help='path to tumor bam file', required = False )
+    parser.add_argument( '--isSkipDepthFilters', help='path to tumor bam file', required = False )
+    parser.add_argument( '--maxInputDepth', help='path to tumor bam file', required = False )
+    args = parser.parse_args()
+
+    #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("configuring...", file=sys.stdout)
+    if os.path.exists(analysis_dir):
+	sys.exit("'" + analysis_dir + "' already exist, if you are executing this tool from galaxy it should not happen")
+    
+
+    # creating index if needed
+    os.environ['PATH']= root_dir + "/opt/samtools:" + os.environ['PATH']
+    bam_filenames = [ args.tumorBam, args.normalBam ]
+    index_bam_files( bam_filenames, tmp_dir )
+    fasta_files = [ args.refFile ]
+    index_fasta_files( fasta_files, tmp_dir )
+    
+    #creating config file if needed
+    if args.configFile == "Custom":
+    	_create_config(vars(args), config_ini)
+    elif args.configFile == "Default":
+        cmdbash="cp %s %s" % (root_dir + "/strelka_config.sample", config_ini)
+        my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
+    else:
+    	if not os.path.exists(args.configFile):
+	     print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr)
+    	cmdbash="cp %s %s" % (args.configFile, config_ini)
+        my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed")
+
+
+
+
+    #configuration of workflow
+    cmd="%s --tumor=%s --normal=%s --ref=%s --config=%s --output-dir=%s" % (config_script, args.tumorBam, args.normalBam, args.refFile, config_ini, analysis_dir)
+    print( "**** Starting configuration.")
+    print( "**** Configuration cmd: '" + cmd + "'")
+    my_Popen( cmd, "cinfugation_stderr", tmp_dir, "Error during configuration !")
+    print("completed configuration")
+    
+    #run the workflow !
+    cmd="make -C " + analysis_dir
+    print("**** starting workflow.")
+    print("**** workflow cmd: '" + cmd + "'")
+    my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !")   
+    print("**** completed workflow execution")
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+#bam_filenames = []
+#    if options.datasets:
+#        for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
+#            gatk_filename = filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )#return the link to the dataset that has been created in the function
+#            if dataset_arg:
+#                cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename )
+#            if galaxy_ext == "bam":
+#                bam_filenames.append( gatk_filename )
+#    #set up stdout and stderr output options
+#    stdout = open_file_from_option( options.stdout, mode = 'wb' )
+#    stderr = open_file_from_option( options.stderr, mode = 'wb' )
+#    #if no stderr file is specified, we'll use our own
+#    if stderr is None:
+#        stderr = tempfile.NamedTemporaryFile( prefix="strelka-stderr-", dir=tmp_dir )
+#    
+#    proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+#    return_code = proc.wait()
+#    
+#    if return_code:
+#        stderr_target = sys.stderr
+#    else:
+#        stderr_target = sys.stdout
+#    stderr.flush()
+#    stderr.seek(0)
+#    while True:
+#        chunk = stderr.read( CHUNK_SIZE )
+#        if chunk:
+#            stderr_target.write( chunk )
+#        else:
+#            break
+#    stderr.close()
+#    #generate html reports
+#    if options.html_report_from_directory:
+#        for ( html_filename, html_dir ) in options.html_report_from_directory:
+#            html_report_from_directory( open( html_filename, 'wb' ), html_dir )
+#    
+#    cleanup_before_exit( tmp_dir )
+
+if __name__=="__main__": __main__()