# HG changeset patch
# User scisjnu123
# Date 1568285870 14400
# Node ID 7a64eb52b0178cf685f66c2dd8696cbaea022d18
# Parent fa1f3c7464a1c9ce04d8709a3ca2123760ca8e6a
Uploaded
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/analyze_covariates.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/analyze_covariates.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,37 @@
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/base_recalibrator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/base_recalibrator.xml Thu Sep 12 06:57:50 2019 -0400
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/combine_gvcfs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/combine_gvcfs.xml Thu Sep 12 06:57:50 2019 -0400
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+ 0
+ --breakBandsAtMultiplesOf $optionals.breakBandsAtMultiplesOf
+ #end if
+ #end if
+]]>
+
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+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/combine_variants.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/combine_variants.xml Thu Sep 12 06:57:50 2019 -0400
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/gatk.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/gatk.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,179 @@
+
+
+ tool collection Version @VERSION@
+
+ gatk_macros.xml
+ realigner_target_creator.xml
+ indel_realigner.xml
+ base_recalibrator.xml
+ analyze_covariates.xml
+ print_reads.xml
+ haplotype_caller.xml
+ genotype_gvcfs.xml
+ combine_gvcfs.xml
+ combine_variants.xml
+
+
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+ &1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2
+]]>
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+ analysis_type['analysis_type_selector'] == 'RealignerTargetCreator'
+
+
+ analysis_type['analysis_type_selector'] == 'IndelRealigner'
+
+
+ analysis_type['analysis_type_selector'] == 'BaseRecalibrator'
+
+
+ analysis_type['analysis_type_selector'] == 'AnalyzeCovariates'
+
+
+ analysis_type['analysis_type_selector'] == 'PrintReads'
+
+
+ analysis_type['analysis_type_selector'] == 'HaplotypeCaller'
+
+
+ analysis_type['analysis_type_selector'] == 'GenotypeGVCFs'
+
+
+ analysis_type['analysis_type_selector'] == 'CombineGVCFs'
+
+
+ analysis_type['analysis_type_selector'] == 'CombineVariants'
+
+
+
+
+
+ 10.1101/gr.107524.110
+ 10.1038/ng.806
+ 10.1002/0471250953.bi1110s43
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/gatk_macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/gatk_macros.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,166 @@
+
+
+
+
+ gatk
+ GATK_PATH
+ GATK_SITE_OPTIONS
+ package_r_for_gatk_3_4_0
+
+
+
+
+
+
+
+ 3.4-0
+ ${tool.name} - ${analysis_type.analysis_type_selector}
+
+ 1:
+ THREAD_STRING="-nct $cond_threads.nct" &&
+ #end if
+ #if int($cond_threads.nt) > 1:
+ THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" &&
+ #end if
+ #if int($cond_threads.mem) > 0:
+ GATK_MEM=$cond_threads.mem &&
+ #end if
+ #end if
+ java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-}
+]]>
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/generation/gatk.xsl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/generation/gatk.xsl Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,162 @@
+
+
+
+
+
+
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+ tool collection Version @VERSION@
+
+
+ gatk_macros.xml
+
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+<![CDATA[
+ ############################
+ ## import analysis specific preprocessings by using cheetahs internal searchList
+ ## if not defined, ignore
+ ############################
+ #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2]
+ #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"]
+ #include source=$analysisPreprocessing
+ #end if
+
+ ############################
+ ## GATK tool unspecific options
+ ############################
+ @GATK_EXEC@
+
+ --analysis_type ${analysis_type.analysis_type_selector}
+ --reference_sequence ${ref_file.fields.path}
+
+ --log_to_file ${output_log}
+
+ #if $cond_intervals.cond_intervals_enabled
+ #for $interval in $cond_intervals.intervals:
+ --intervals ${interval.L}
+ #end for
+ #end if
+
+ #if $cond_BQSR.cond_BQSR_enabled
+ --BQSR $cond_BQSR.BQSR
+ #end if
+
+ ############################
+ ## import analysis specific options by using cheetahs internal searchList
+ ## if not defined throw raw python error until better idea
+ ############################
+ #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2]
+ #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
+ #include source=$analysisOptions
+ #else
+ #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
+ #end if
+
+ ############################
+ ## only put ERROR or FATAL log messages into stderr
+ ## but keep full log for printing into log file
+ ############################
+ 2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2
+]]>
+
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+ analysis_type['analysis_type_selector'] == ''
+
+
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+
+
+
+
+ 10.1101/gr.107524.110
+ 10.1038/ng.806
+ 10.1002/0471250953.bi1110s43
+
+
+
+
+
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/generation/gatk.xsldb.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/generation/gatk.xsldb.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,57 @@
+
+
+
+ RealignerTargetCreator
+ bam
+ rtc
+ realigner_target_creator.xml
+
+
+ IndelRealigner
+ bam
+ ir
+ indel_realigner.xml
+
+
+ BaseRecalibrator
+ bam
+ br
+ base_recalibrator.xml
+
+
+ AnalyzeCovariates
+ bam
+ ac
+ analyze_covariates.xml
+
+
+ PrintReads
+ bam
+ pr
+ print_reads.xml
+
+
+ HaplotypeCaller
+ bam
+ hc
+ haplotype_caller.xml
+
+
+ GenotypeGVCFs
+ gvcf
+ gg
+ genotype_gvcfs.xml
+
+
+ CombineGVCFs
+ gvcf
+ cg
+ combine_gvcfs.xml
+
+
+ CombineVariants
+ vcf
+ cv
+ combine_variants.xml
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/genotype_gvcfs.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/genotype_gvcfs.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,43 @@
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/haplotype_caller.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/haplotype_caller.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,65 @@
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/indel_realigner.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/indel_realigner.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,90 @@
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/print_reads.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/print_reads.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,71 @@
+
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+ 0
+ --number $optionals.number
+ #end if
+ #if str($optionals.platform)
+ --platform $optionals.platform
+ #end if
+ #if str($optionals.readGroup)
+ --readGroup $optionals.readGroup
+ #end if
+ #if $optionals.sample_file
+ --sample_file $optionals.sample_file
+ #end if
+ #if $optionals.sample_names
+ #for $sample in $optionals.sample_names:
+ --intervals ${sample.sample_name}
+ #end for
+ #end if
+ $optionals.simplify
+ #end if
+]]>
+
+
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/realigner_target_creator.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/realigner_target_creator.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,57 @@
+
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diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/tool-data/destinations.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool-data/destinations.py Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,62 @@
+from galaxy.jobs import JobDestination
+import os
+import sys
+import json
+import cStringIO
+import logging
+
+log = logging.getLogger( __name__ )
+
+
+def dump(obj, nested_level=0, output=sys.stdout):
+ spacing = ' '
+ if type(obj) == dict:
+ print >> output, '%s{' % ((nested_level) * spacing)
+ for k, v in obj.items():
+ if hasattr(v, '__iter__'):
+ print >> output, '%s%s:' % ((nested_level + 1) * spacing, k)
+ dump(v, nested_level + 1, output)
+ else:
+ print >> output, '%s%s: %s' % ((nested_level + 1) * spacing, k, v)
+ print >> output, '%s}' % (nested_level * spacing)
+ elif type(obj) == list:
+ print >> output, '%s[' % ((nested_level) * spacing)
+ for v in obj:
+ if hasattr(v, '__iter__'):
+ dump(v, nested_level + 1, output)
+ else:
+ print >> output, '%s%s' % ((nested_level + 1) * spacing, v)
+ print >> output, '%s]' % ((nested_level) * spacing)
+ else:
+ print >> output, '%s%s' % (nested_level * spacing, obj)
+
+
+def dynamic_slurm_cluster_gatk(job, tool_id):
+ # Allocate extra time
+ inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
+ inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
+ inp_data.update( [ ( da.name, json.loads(da.value) ) for da in job.parameters ] )
+ out = cStringIO.StringIO()
+ dump(inp_data, 1, out)
+ log.debug(out.getvalue())
+
+ nativeSpecs = '--nodes=1 --ntasks=1'
+
+ # runner doesn't allow to specify --cpus-per-task
+ # thus the mem calculation gets messy with more than 1 node
+ # --> translate nt ==> nodes, nct ==> ntasks
+
+ if 'cond_threads' not in inp_data:
+ return JobDestination(runner="slurm")
+
+ if inp_data['cond_threads']['cond_threads_enabled'] == "True":
+ nNodes = int(inp_data['cond_threads']['nt'])
+ nCPU = int(inp_data['cond_threads']['nct'])
+ nMEM = int(inp_data['cond_threads']['mem'])
+ if nMEM > 0:
+ nativeSpecs = '--nodes=%d --ntasks=%d --mem=%d' % (nNodes, nCPU*nNodes, nMEM)
+ else:
+ nativeSpecs = '--nodes=%d --ntasks=%d' % (nNodes, nCPU*nNodes)
+
+ return JobDestination(runner="slurm", params={"nativeSpecification": nativeSpecs})
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/tool-data/picard_index.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool-data/picard_index.loc.sample Thu Sep 12 06:57:50 2019 -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 fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool_data_table_conf.xml.sample Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/gatk/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool_dependencies.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,19 @@
+
+
+
+ /mnt/galaxy/tools/GATK/3.4-0
+
+
+
+
+
+
+
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/package_picard_1_135/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/package_picard_1_135/tool_dependencies.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,22 @@
+
+
+
+
+
+
+ https://github.com/broadinstitute/picard/releases/download/1.135/picard-tools-1.135.zip
+
+ .
+ $INSTALL_DIR
+
+
+
+ $INSTALL_DIR
+
+
+
+
+This picard package dependency is retrieved directly from https://github.com/broadinstitute/picard/releases
+
+
+
diff -r fa1f3c7464a1 -r 7a64eb52b017 GATK/package_r_for_gatk_3_4_0/tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/package_r_for_gatk_3_4_0/tool_dependencies.xml Thu Sep 12 06:57:50 2019 -0400
@@ -0,0 +1,48 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+ https://github.com/cran/stringi/archive/0.5-5.tar.gz
+ https://github.com/cran/magrittr/archive/1.5.tar.gz
+ https://github.com/cran/stringr/archive/1.0.0.tar.gz
+ https://github.com/cran/RColorBrewer/archive/1.1-2.tar.gz
+ https://github.com/cran/dichromat/archive/2.0-0.tar.gz
+ https://github.com/cran/colorspace/archive/1.2-6.tar.gz
+ https://github.com/cran/munsell/archive/0.4.2.tar.gz
+ https://github.com/cran/labeling/archive/0.3.tar.gz
+ https://github.com/cran/Rcpp/archive/0.11.6.tar.gz
+ https://github.com/cran/digest/archive/0.6.8.tar.gz
+ https://github.com/cran/gtable/archive/0.1.2.tar.gz
+ https://github.com/cran/bitops/archive/1.0-6.tar.gz
+ https://github.com/cran/caTools/archive/1.17.1.tar.gz
+ https://github.com/cran/gtools/archive/3.5.0.tar.gz
+ https://github.com/cran/gdata/archive/2.17.0.tar.gz
+ https://github.com/cran/gsalib/archive/2.1.tar.gz
+ https://github.com/cran/gplots/archive/2.17.0.tar.gz
+ https://github.com/cran/plyr/archive/1.8.3.tar.gz
+ https://github.com/cran/reshape/archive/0.8.5.tar.gz
+ https://github.com/cran/reshape2/archive/1.4.1.tar.gz
+ https://github.com/cran/scales/archive/0.2.5.tar.gz
+ https://github.com/cran/proto/archive/0.3-10.tar.gz
+ https://github.com/cran/MASS/archive/7.3-43.tar.gz
+ https://github.com/cran/ggplot2/archive/1.0.1.tar.gz
+
+
+
+
+ ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and none of the bad parts.
+ It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics.
+
+ http://ggplot2.org/
+
+
+