1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/218ca2b7e446/ changeset: 218ca2b7e446 user: dan date: 2011-10-06 18:27:48 summary: Some gatk_wrapper.py tweaks. affected #: 1 file (-1 bytes) --- a/tools/gatk/gatk_wrapper.py Thu Oct 06 12:16:48 2011 -0400 +++ b/tools/gatk/gatk_wrapper.py Thu Oct 06 12:27:48 2011 -0400 @@ -8,7 +8,7 @@ import sys, optparse, os, tempfile, subprocess, shutil from string import Template -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_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 @@ -48,21 +48,21 @@ parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' ) parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' ) parser.add_option( '', '--max_jvm_heap', dest='max_jvm_heap', action='store', type="string", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value.' ) - parser.add_option( '', '--max_jvm_heap_fraction', dest='max_jvm_heap_fraction', action='store', type="int", default=0, help='If specified, the maximum java virtual machine heap size will be set to the provide value as a fraction of total physical memory.' ) + parser.add_option( '', '--max_jvm_heap_fraction', dest='max_jvm_heap_fraction', action='store', type="int", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value as a fraction of total physical memory.' ) parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' ) parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"') (options, args) = parser.parse_args() - tmp_dir = tempfile.mkdtemp() + tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' ) if options.pass_through_options: cmd = ' '.join( options.pass_through_options ) else: cmd = '' - if options.max_jvm_heap: - cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 ) - elif options.max_jvm_heap_fraction: - cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 ) + if options.max_jvm_heap is not None: + cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 ) + elif options.max_jvm_heap_fraction is not None: + cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 ) if options.datasets: for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets: gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix ) @@ -73,9 +73,7 @@ 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( dir=tmp_dir ) - stderr.close() - stderr = open( stderr.name, 'w+b' ) + stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir ) proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) return_code = proc.wait() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.