# HG changeset patch
# User devteam
# Date 1396363706 14400
# Node ID bb0beda6cf832707f0a4a03fa36a526da6b6bc91
Imported from capsule None
diff -r 000000000000 -r bb0beda6cf83 gatk_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gatk_macros.xml Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,305 @@
+
+
+ ##start standard gatk options
+ #if $gatk_param_type.gatk_param_type_selector == "advanced":
+ #for $pedigree in $gatk_param_type.pedigree:
+ -p '--pedigree "${pedigree.pedigree_file}"'
+ #end for
+ #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
+ -p '--pedigreeString "${pedigree_string.pedigree_string}"'
+ #end for
+ -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+ #for $read_filter in $gatk_param_type.read_filter:
+ -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+ ###raise Exception( str( dir( $read_filter ) ) )
+ #for $name, $param in $read_filter.read_filter_type.iteritems():
+ #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
+ #if hasattr( $param.input, 'truevalue' ):
+ ${param}
+ #else:
+ --${name} "${param}"
+ #end if
+ #end if
+ #end for
+ '
+ #end for
+ #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_interval_repeat ):
+ -d "--intervals" "${input_intervals.input_intervals}" "${input_intervals.input_intervals.ext}" "input_intervals_${interval_count}"
+ #end for
+
+ #for $interval_count, $input_intervals in enumerate( $gatk_param_type.input_exclude_interval_repeat ):
+ -d "--excludeIntervals" "${input_intervals.input_exclude_intervals}" "${input_intervals.input_exclude_intervals.ext}" "input_exlude_intervals_${interval_count}"
+ #end for
+
+ -p '--interval_set_rule "${gatk_param_type.interval_set_rule}"'
+
+ -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
+ #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
+ -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
+ #end if
+ -p '
+ --baq "${gatk_param_type.baq}"
+ --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
+ ${gatk_param_type.use_original_qualities}
+ --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
+ --validation_strictness "${gatk_param_type.validation_strictness}"
+ --interval_merging "${gatk_param_type.interval_merging}"
+ ${gatk_param_type.disable_experimental_low_memory_sharding}
+ ${gatk_param_type.non_deterministic_random_seed}
+ '
+ #for $rg_black_list_count, $rg_black_list in enumerate( $gatk_param_type.read_group_black_list_repeat ):
+ #if $rg_black_list.read_group_black_list_type.read_group_black_list_type_selector == "file":
+ -d "--read_group_black_list" "${rg_black_list.read_group_black_list_type.read_group_black_list}" "txt" "input_read_group_black_list_${rg_black_list_count}"
+ #else
+ -p '--read_group_black_list "${rg_black_list.read_group_black_list_type.read_group_black_list}"'
+ #end if
+ #end for
+ #end if
+
+ #if str( $reference_source.reference_source_selector ) == "history":
+ -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
+ #end if
+ ##end standard gatk options
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+ ------
+
+**Citation**
+
+For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. <http://www.ncbi.nlm.nih.gov/pubmed/21478889>`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+
+
\ No newline at end of file
diff -r 000000000000 -r bb0beda6cf83 gatk_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/gatk_wrapper.py Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,126 @@
+#!/usr/bin/env python
+#Dan Blankenberg
+
+"""
+A wrapper script for running the GenomeAnalysisTK.jar commands.
+"""
+
+import sys, optparse, os, tempfile, subprocess, shutil
+from binascii import unhexlify
+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_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 gatk_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ):
+ suffix = GALAXY_EXT_TO_GATK_EXT.get( galaxy_ext, galaxy_ext )
+ if prefix is None:
+ prefix = DEFAULT_GATK_PREFIX
+ if target_dir is None:
+ target_dir = os.getcwd()
+ gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) )
+ os.symlink( galaxy_filename, gatk_filename )
+ return gatk_filename
+
+def gatk_filetype_argument_substitution( argument, galaxy_ext ):
+ return argument % dict( file_type = GALAXY_EXT_TO_GATK_FILE_TYPE.get( galaxy_ext, galaxy_ext ) )
+
+def open_file_from_option( filename, mode = 'rb' ):
+ if filename:
+ return open( filename, mode = mode )
+ return None
+
+def html_report_from_directory( html_out, dir ):
+ html_out.write( '\n\nGalaxy - GATK Output\n\n\n\n\n' )
+ for fname in sorted( os.listdir( dir ) ):
+ html_out.write( '- %s
\n' % ( fname, fname ) )
+ html_out.write( '
\n\n\n' )
+
+def index_bam_files( bam_filenames, tmp_dir ):
+ for bam_filename in bam_filenames:
+ bam_index_filename = "%s.bai" % bam_filename
+ if not os.path.exists( bam_index_filename ):
+ #need to index this bam file
+ stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
+ command = 'samtools index %s %s' % ( bam_filename, bam_index_filename )
+ proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
+ return_code = proc.wait()
+ if return_code:
+ for line in open( stderr_name ):
+ print >> sys.stderr, line
+ os.unlink( stderr_name ) #clean up
+ cleanup_before_exit( tmp_dir )
+ raise Exception( "Error indexing BAM file" )
+ os.unlink( stderr_name ) #clean up
+
+def __main__():
+ #Parse Command Line
+ parser = optparse.OptionParser()
+ 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( '-o', '--pass_through_options', dest='pass_through_options_encoded', action='append', type="string", help='These options are passed through directly to GATK, with decoding from binascii.unhexlify.' )
+ 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=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( prefix='tmp-gatk-' )
+ if options.pass_through_options:
+ cmd = ' '.join( options.pass_through_options )
+ else:
+ cmd = ''
+ if options.pass_through_options_encoded:
+ cmd = '%s %s' % ( cmd, ' '.join( map( unhexlify, options.pass_through_options_encoded ) ) )
+ 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 )
+ bam_filenames = []
+ 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 )
+ 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 )
+ index_bam_files( bam_filenames, tmp_dir )
+ #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="gatk-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__()
diff -r 000000000000 -r bb0beda6cf83 indel_realigner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/indel_realigner.xml Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,209 @@
+
+ - perform local realignment
+
+ gatk
+ samtools
+
+
+ gatk_macros.xml
+
+ gatk_wrapper.py
+ --max_jvm_heap_fraction "1"
+ --stdout "${output_log}"
+ -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+ #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+ -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+ #end if
+ -p 'java
+ -jar "\$JAVA_JAR_PATH/GenomeAnalysisTK.jar"
+ -T "IndelRealigner"
+ -o "${output_bam}"
+ -et "NO_ET" ##ET no phone home
+ ##--num_threads 4 ##hard coded, for now
+ ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+ #if $reference_source.reference_source_selector != "history":
+ -R "${reference_source.ref_file.fields.path}"
+ #end if
+ -LOD "${lod_threshold}"
+ ${knowns_only}
+ '
+
+ #set $rod_binding_names = dict()
+ #for $rod_binding in $rod_bind:
+ #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
+ #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
+ #else
+ #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
+ #end if
+ #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
+ -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}"
+ #end for
+
+ #include source=$standard_gatk_options#
+ ##start analysis specific options
+ -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
+ -p '
+ --disable_bam_indexing
+ '
+ #if $analysis_param_type.analysis_param_type_selector == "advanced":
+ -p '
+ --entropyThreshold "${analysis_param_type.entropy_threshold}"
+ ${analysis_param_type.simplify_bam}
+ --consensusDeterminationModel "${analysis_param_type.consensus_determination_model}"
+ --maxIsizeForMovement "${analysis_param_type.max_insert_size_for_movement}"
+ --maxPositionalMoveAllowed "${analysis_param_type.max_positional_move_allowed}"
+ --maxConsensuses "${analysis_param_type.max_consensuses}"
+ --maxReadsForConsensuses "${analysis_param_type.max_reads_for_consensuses}"
+ --maxReadsForRealignment "${analysis_param_type.max_reads_for_realignment}"
+ ${analysis_param_type.no_original_alignment_tags}
+ '
+ #end if
+
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+**What it does**
+
+Performs local realignment of reads based on misalignments due to the presence of indels. Unlike most mappers, this walker uses the full alignment context to determine whether an appropriate alternate reference (i.e. indel) exists and updates SAMRecords accordingly.
+
+For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels>`_.
+
+To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_.
+
+If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
+
+------
+
+**Inputs**
+
+GenomeAnalysisTK: IndelRealigner accepts an aligned BAM and a list of intervals to realign as input files.
+
+
+**Outputs**
+
+The output is in the BAM format.
+
+
+Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+ targetIntervals intervals file output from RealignerTargetCreator
+ LODThresholdForCleaning LOD threshold above which the cleaner will clean
+ entropyThreshold percentage of mismatches at a locus to be considered having high entropy
+ out Output bam
+ bam_compression Compression level to use for writing BAM files
+ disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files.
+ simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
+ useOnlyKnownIndels Don't run 'Smith-Waterman' to generate alternate consenses; use only known indels provided as RODs for constructing the alternate references.
+ maxReadsInMemory max reads allowed to be kept in memory at a time by the SAMFileWriter. Keep it low to minimize memory consumption (but the tool may skip realignment on regions with too much coverage. If it is too low, it may generate errors during realignment); keep it high to maximize realignment (but make sure to give Java enough memory).
+ maxIsizeForMovement maximum insert size of read pairs that we attempt to realign
+ maxPositionalMoveAllowed maximum positional move in basepairs that a read can be adjusted during realignment
+ maxConsensuses max alternate consensuses to try (necessary to improve performance in deep coverage)
+ maxReadsForConsensuses max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)
+ maxReadsForRealignment max reads allowed at an interval for realignment; if this value is exceeded, realignment is not attempted and the reads are passed to the output file(s) as-is
+ noOriginalAlignmentTags Don't output the original cigar or alignment start tags for each realigned read in the output bam.
+
+@CITATION_SECTION@
+
+
diff -r 000000000000 -r bb0beda6cf83 test-data/1.bam
Binary file test-data/1.bam has changed
diff -r 000000000000 -r bb0beda6cf83 test-data/a.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a.tab Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,15 @@
+CHR SNP BP A1 TEST NMISS BETA STAT P
+1 rs1181876 3671541 T DOMDEV 958 -1.415 -3.326 0.0009161
+1 rs10492923 5092886 C ADD 1007 5.105 4.368 1.382e-05
+1 rs10492923 5092886 C DOMDEV 1007 -5.612 -4.249 2.35e-05
+1 rs10492923 5092886 C GENO_2DF 1007 NA 19.9 4.775e-05
+1 rs1801133 11778965 T ADD 1022 1.23 3.97 7.682e-05
+1 rs1801133 11778965 T GENO_2DF 1022 NA 16.07 0.0003233
+1 rs1361912 12663121 A ADD 1021 12.69 4.093 4.596e-05
+1 rs1361912 12663121 A DOMDEV 1021 -12.37 -3.945 8.533e-05
+1 rs1361912 12663121 A GENO_2DF 1021 NA 17.05 0.0001982
+1 rs1009806 19373138 G ADD 1021 -1.334 -3.756 0.0001826
+1 rs1009806 19373138 G GENO_2DF 1021 NA 19.36 6.244e-05
+1 rs873654 29550948 A DOMDEV 1012 1.526 3.6 0.0003339
+1 rs10489527 36800027 C ADD 1016 12.67 4.114 4.211e-05
+1 rs10489527 36800027 C DOMDEV 1016 -13.05 -4.02 6.249e-05
diff -r 000000000000 -r bb0beda6cf83 test-data/gatk/fake_phiX_reads_1.bam
Binary file test-data/gatk/fake_phiX_reads_1.bam has changed
diff -r 000000000000 -r bb0beda6cf83 test-data/gatk/fake_phiX_variant_locations.vcf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/fake_phiX_variant_locations.vcf Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.18 (r982:295)
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##INFO=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+##FORMAT=
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample
+phiX174 1411 . A . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0
+phiX174 1412 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0
+phiX174 1413 . C . 28.2 . DP=5;;AC1=2;FQ=-30 PL 0
+phiX174 1414 . G . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0
+phiX174 1415 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0
+phiX174 1416 . C . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0
+phiX174 1417 . G . 28.2 . DP=9;;AC1=2;FQ=-30 PL 0
+phiX174 1418 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1419 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1420 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1421 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1422 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1423 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1424 . C . 28.2 . DP=10;VDB=0.0005;;AC1=2;FQ=-30 PL 0
+phiX174 1425 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1426 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1427 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1428 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1429 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1430 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1431 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1432 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1433 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1434 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1435 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1436 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1437 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1438 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1439 . G . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1440 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1441 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1442 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1443 . A . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1444 . C . 28.2 . DP=7;;AC1=2;FQ=-30 PL 0
+phiX174 1445 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1446 . C . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1447 . T . 28.2 . DP=10;;AC1=2;FQ=-30 PL 0
+phiX174 1448 . A . 28.2 . DP=8;;AC1=2;FQ=-30 PL 0
+phiX174 1449 . A . 28.2 . DP=6;;AC1=2;FQ=-30 PL 0
+phiX174 1450 . T . 28.2 . DP=4;;AC1=2;FQ=-30 PL 0
+phiX174 1451 . G . 28.2 . DP=3;;AC1=2;FQ=-30 PL 0
+phiX174 1452 . A . 28.2 . DP=2;;AC1=2;FQ=-30 PL 0
+phiX174 1453 . G . 28.2 . DP=1;;AC1=2;FQ=-30 PL 0
diff -r 000000000000 -r bb0beda6cf83 test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam
Binary file test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam has changed
diff -r 000000000000 -r bb0beda6cf83 test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,4 @@
+GenomeAnalysisEngine - Strictness is SILENT
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
+TraversalEngine - Total runtime
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%)
\ No newline at end of file
diff -r 000000000000 -r bb0beda6cf83 test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,1 @@
+phiX174:1446-1447
diff -r 000000000000 -r bb0beda6cf83 test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+
diff -r 000000000000 -r bb0beda6cf83 tool-data/gatk_sorted_picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/gatk_sorted_picard_index.loc.sample Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#So, for example, if you had hg18 indexed and stored in
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff -r 000000000000 -r bb0beda6cf83 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,8 @@
+
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r bb0beda6cf83 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Apr 01 10:48:26 2014 -0400
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+