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Some gatk_wrapper.py tweaks.

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This commit is contained in:
Daniel Blankenberg
2011-10-06 12:27:48 -04:00
parent c87682305d
commit 8fa20276b4
1 changed files with 8 additions and 10 deletions
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tools/gatk/gatk_wrapper.py
+8 -10
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@@ -8,7 +8,7 @@ A wrapper script for running the GenomeAnalysisTK.jar commands.
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 @@ def __main__():
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 @@ def __main__():
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()