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Remove bam index metadata validator from GATK tools. The GATK wrapper will now build missing bam indexes on the fly as needed.

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Daniel Blankenberg
2012-02-27 12:49:30 -05:00
parent 2e6e3b2118
commit 3fbcb4bfc1
10 changed files with 54 additions and 25 deletions
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tools/gatk/analyze_covariates.xml
+1 -1
View File
@@ -74,7 +74,7 @@ GenomeAnalysisTK: AnalyzeCovariates accepts an recal CSV file.
**Outputs**
The output is in and HTML file with links to PDF graphs and a data files.
The output is in CSV and HTML files with links to PDF graphs and a data files.
Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
tools/gatk/count_covariates.xml
+4 -3
View File
@@ -2,12 +2,15 @@
<description>on BAM files</description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
-d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
#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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "CountCovariates"
@@ -143,7 +146,6 @@
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
<param name="ref_file" type="select" label="Using reference genome">
@@ -155,7 +157,6 @@
</when>
<when value="history"> <!-- FIX ME!!!! -->
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
</when>
tools/gatk/depth_of_coverage.xml
+4 -3
View File
@@ -2,13 +2,16 @@
<description>on BAM files</description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#end if
#end for
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
@@ -190,7 +193,6 @@
<repeat name="input_bams" title="BAM file" min="1">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
</repeat>
@@ -204,7 +206,6 @@
<when value="history"> <!-- FIX ME!!!! -->
<repeat name="input_bams" title="BAM file" min="1">
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
</repeat>
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
tools/gatk/gatk_wrapper.py
+21
View File
@@ -43,6 +43,23 @@ def html_report_from_directory( html_out, dir ):
html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
html_out.write( '</ul>\n</body>\n</html>\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()
@@ -67,11 +84,15 @@ def __main__():
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' )
tools/gatk/indel_realigner.xml
+4 -3
View File
@@ -2,12 +2,15 @@
<description>- perform local realignment</description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
-d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
#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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "IndelRealigner"
@@ -121,7 +124,6 @@
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
<param name="ref_file" type="select" label="Using reference genome">
@@ -133,7 +135,6 @@
</when>
<when value="history"> <!-- FIX ME!!!! -->
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
<param name="ref_file" type="data" format="fasta" label="Using reference file">
<options>
tools/gatk/print_reads.xml
+4 -3
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@@ -2,13 +2,16 @@
<description>from BAM files</description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#end if
#end for
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
@@ -106,7 +109,6 @@
<repeat name="input_bams" title="Sample BAM file" min="1">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
</repeat>
@@ -120,7 +122,6 @@
<when value="history"> <!-- FIX ME!!!! -->
<repeat name="input_bams" title="Sample BAM file" min="1">
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
</repeat>
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
tools/gatk/realigner_target_creator.xml
+4 -3
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@@ -2,12 +2,15 @@
<description>for use in local realignment</description>
<requirements>
<requirement type="package" version="1.3">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
-d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
#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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "RealignerTargetCreator"
@@ -109,7 +112,6 @@
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
<param name="ref_file" type="select" label="Using reference genome">
@@ -121,7 +123,6 @@
</when>
<when value="history">
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
<param name="ref_file" type="data" format="fasta" label="Using reference file">
<options>
tools/gatk/table_recalibration.xml
+4 -3
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@@ -2,12 +2,15 @@
<description>on BAM files</description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
-d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
#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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
-T "TableRecalibration"
@@ -126,7 +129,6 @@
<when value="cached">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
<param name="ref_file" type="select" label="Using reference genome">
@@ -138,7 +140,6 @@
</when>
<when value="history"> <!-- FIX ME!!!! -->
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
</when>
tools/gatk/unified_genotyper.xml
+4 -3
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@@ -2,13 +2,16 @@
<description>SNP and indel caller</description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
#for $i, $input_bam in enumerate( $reference_source.input_bams ):
-d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
#end if
#end for
-p 'java
-jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
@@ -155,7 +158,6 @@
<repeat name="input_bams" title="Sample BAM file" min="1">
<param name="input_bam" type="data" format="bam" label="BAM file">
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
</repeat>
@@ -169,7 +171,6 @@
<when value="history"> <!-- FIX ME!!!! -->
<repeat name="input_bams" title="Sample BAM file" min="1">
<param name="input_bam" type="data" format="bam" label="BAM file" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
</repeat>
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
tools/gatk/variant_annotator.xml
+4 -3
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@@ -2,13 +2,16 @@
<description></description>
<requirements>
<requirement type="package" version="1.4">gatk</requirement>
<requirement type="package">samtools</requirement>
</requirements>
<command interpreter="python">gatk_wrapper.py
--max_jvm_heap_fraction "1"
--stdout "${output_log}"
#if str( $reference_source.input_bam ) != "None":
-d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
#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
#end if
-d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
-p 'java
@@ -151,7 +154,6 @@
<param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
<param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations." >
<validator type="unspecified_build" />
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
<validator type="dataset_metadata_in_data_table" table_name="gatk_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
</param>
<param name="ref_file" type="select" label="Using reference genome">
@@ -165,7 +167,6 @@
<param name="input_variant" type="data" format="vcf" label="Variant file to annotate" />
<param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." />
<param name="input_bam" type="data" format="bam" label="BAM file" optional="True" >
<validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
</param>
<param name="ref_file" type="data" format="fasta" label="Using reference file" />
</when>