mutations_caller_pipeline_aws 0.0.6
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- data/bin/gatk_pipe_only_aws +168 -0
- data/bin/mutations_caller_pipeline_aws +196 -0
- data/lib/mutations_caller_pipeline_aws/.DS_Store +0 -0
- data/lib/mutations_caller_pipeline_aws/bwa_caller.rb +18 -0
- data/lib/mutations_caller_pipeline_aws/gatk_caller.rb +70 -0
- data/lib/mutations_caller_pipeline_aws/location_file.rb +21 -0
- data/lib/mutations_caller_pipeline_aws/samtools_indexing.rb +8 -0
- data/lib/mutations_caller_pipeline_aws.rb +11 -0
- metadata +56 -0
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#!/usr/bin/env ruby
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require 'mutations_caller_pipeline_aws'
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require 'optparse'
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require 'rubygems'
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require 'yaml'
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usage =<<EOF
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_________________________________________________________________________________________________
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#{$0}
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-b sorted_bam_file
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-c config.yml -v raw_vcf_file
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[-a account || -p project]
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_________________________________________________________________________________________________
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#{$0} ...
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... is a tool to find mutations between the reference gene and a given test
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population. To run this tool you must have bwa, samtools and GATK installed.
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Also you should have the indices for bwa and GATK prepared.
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NOTE: Only paired end reads are supported!
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+++ C L U S T E R V E R S I O N +++
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config.yml should look like this:
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# config.yml
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index_prefix: "path/to/prefix"
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annotation_file: "path/to/annotation_file"
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bwa: "path/to/bwa"
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samtools: "path/to/samtools"
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gatk: "path/to/GenomeAnalysisTK.jar"
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_________________________________________________________________________________________________
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EOF
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options = { :bam_file_sorted => nil,
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:index_prefix => nil,
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:index_fa => nil,
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:index_vcf => nil,
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:annotation_file => nil,
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:samtools => nil,
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:gatk => nil,
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:bwa => nil,
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:vcf => nil,
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:account => "",
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:project => "",
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:debug = 1,
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}
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optparse = OptionParser.new do |opts|
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opts.banner = usage
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opts.on("-b", "--bam_file_sorted DIR", :REQUIRED, String, "Bam file sorted") do |i|
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options[:bam_file_sorted] = i
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end
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opts.on("-c", "--config DIR",:REQUIRED, String, "Set config file") do |path|
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options.merge!(Hash[YAML::load(open(path)).map { |k, v| [k.to_sym, v] }])
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end
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opts.on("-v","--vcf [PATH]",:REQUIRED, String, "Output of pipeline") do |i|
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options[:vcf] = i
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end
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opts.on("-a","--account [NAME]", "Option for qsub: -A [NAME]. Default: [none] " ) do |i|
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options[:account] = " -A #{i}" if i
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end
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opts.on("-p","--project [NAME]", "Option for qsub: -P [NAME]. Default: [none] " ) do |i|
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options[:project] = " -P #{i}" if i
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end
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opts.on("-d","--debug ", "Option to debug" ) do |i|
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options[:debug] = 5 if i
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end
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opts.on_tail("-h", "--help", "Show this message") do
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puts opts
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exit
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end
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end
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begin
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optparse.parse!
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mandatory = [:bam_file_sorted, :index_prefix, :annotation_file, :bwa, :samtools, :gatk, :vcf, :index_vcf, :index_fa]
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missing = mandatory.select{ |param| options[param].nil? }
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if !missing.empty?
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puts "\nMissing options given or missing in config_file: \n\t#{missing.join(",\n\t")}"
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puts optparse
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exit
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end
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rescue OptionParser::InvalidOption, OptionParser::MissingArgument
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puts $!.to_s
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puts optparse
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exit
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end
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# pipeline starts here
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# tmp files for output
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random = (rand*1000000).floor.to_s
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bam_file = options[:bam_file_sorted]
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job_prefix = "#{random}"
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log_file = "#{random}.log"
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target_intervals = "#{random}_target.intervals"
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realigned_bam = "#{random}_realigned.bam"
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recal_file = "#{random}_recal.csv"
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recal_bam = "#{random}_recal.bam"
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options[:account] = options[:project] if options[:account].empty?
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# Indexing
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SamtoolsIndexing.call(bam_file,
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job_prefix,
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account,
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options[:debug])
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# Realigne
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GatkCaller.prepare_realigne(log_file,
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options[:gatk],
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bam_file,
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options[:index_fa],
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target_intervals,
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job_prefix,
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options[:account],
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options[:debug])
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GatkCaller.realigne(log_file,
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options[:gatk],
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bam_file,
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options[:index_fa],
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target_intervals,
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realigned_bam,
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job_prefix,
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options[:account],
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options[:debug])
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# Recalibration
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GatkCaller.recalibrate_bam( log_file,
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options[:gatk],
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options[:index_fa],
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options[:index_vcf],
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realigned_bam,
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recal_file,
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job_prefix,
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options[:account],
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options[:debug] )
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GatkCaller.table_calibration(log_file,
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options[:gatk],
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options[:index_fa],
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realigned_bam,
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recal_bam,
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recal_file,
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job_prefix,
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options[:account],
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options[:debug])
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# GATK: finding mutations
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GatkCaller.call(log_file,
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options[:gatk],
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options[:index_fa],
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recal_bam,
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options[:vcf],
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job_prefix,
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options[:account],
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options[:debug])
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#!/usr/bin/env ruby
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require 'mutations_caller_pipeline_aws'
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require 'optparse'
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require 'rubygems'
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require 'yaml'
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usage =<<EOF
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_________________________________________________________________________________________________
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#{$0}
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-m mutant_r1.fq -n mutant_r2.fq
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[-w wildtype_r1.fq -x wildtype_r2.fq]
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-c config.yml -v raw_vcf_file
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[-a account || -p project]
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_________________________________________________________________________________________________
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#{$0} ...
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... is a tool to find mutations between the reference gene and a given test
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population. To run this tool you must have bwa, samtools and GATK installed.
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Also you should have the indices for bwa and GATK prepared.
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NOTE: Only paired end reads are supported!
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+
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+++ C L U S T E R V E R S I O N +++
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config.yml should look like this:
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# config.yml
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index_prefix: "path/to/prefix"
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annotation_file: "path/to/annotation_file"
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bwa: "path/to/bwa"
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samtools: "path/to/samtools"
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gatk: "path/to/GenomeAnalysisTK.jar"
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_________________________________________________________________________________________________
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EOF
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options = { :mutant_r1 => nil,
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:mutant_r2 => nil,
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:wildtype_r1 => nil,
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:wildtype_r2 => nil,
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:index_prefix => nil,
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:index_fa => nil,
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:index_vcf => nil,
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:annotation_file => nil,
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:samtools => nil,
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:gatk => nil,
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:bwa => nil,
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:vcf => nil,
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:account => "",
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:project => "",
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:debug => 1,
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}
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optparse = OptionParser.new do |opts|
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opts.banner = usage
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opts.on("-m", "--fwd_read_mutant DIR", :REQUIRED, String, "Path to fwd read of mutant") do |i|
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options[:mutant_r1] = i
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end
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opts.on("-n", "--rev_read_mutant DIR", :REQUIRED, String, "Path to rev read of mutant") do |i|
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options[:mutant_r2] = i
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end
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opts.on("-w", "--fwd_read_wildtype DIR", String, "Path to fwd read of wildtype, not mandatory") do |i|
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options[:wildtype_r1] = i if i
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end
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opts.on("-x", "--rev_read_wildtype DIR", String, "Path to rev read of wildtype, not mandatory") do |i|
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options[:wildtype_r2] = i if i
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end
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opts.on("-c", "--config DIR", String, "Set config file") do |path|
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options.merge!(Hash[YAML::load(open(path)).map { |k, v| [k.to_sym, v] }])
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end
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opts.on("-v","--vcf [PATH]", "Output of pipeline") do |i|
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options[:vcf] = i
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end
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opts.on("-a","--account [NAME]", "Option for qsub: -A [NAME]. Default: [none] " ) do |i|
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options[:account] = " -A #{i}" if i
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end
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opts.on("-p","--project [NAME]", "Option for qsub: -P [NAME]. Default: [none] " ) do |i|
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options[:project] = " -P #{i}" if i
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end
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opts.on("-d","--debug ", "Option to debug" ) do |i|
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options[:debug] = 5 if i
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end
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opts.on_tail("-h", "--help", "Show this message") do
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puts opts
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exit
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end
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end
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begin
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optparse.parse!
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mandatory = [:mutant_r1, :mutant_r2, :index_prefix, :annotation_file, :bwa, :samtools, :gatk, :vcf, :index_vcf, :index_fa]
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missing = mandatory.select{ |param| options[param].nil? }
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if !missing.empty?
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puts "\nMissing options given or missing in config_file: \n\t#{missing.join(",\n\t")}"
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puts optparse
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exit
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end
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rescue OptionParser::InvalidOption, OptionParser::MissingArgument
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puts $!.to_s
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puts optparse
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exit
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end
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# pipeline starts here
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# tmp files for output
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random = (rand*1000000).floor.to_s
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bam_file = "mutant_#{random}"
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job_prefix = "#{random}"
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log_file = "#{random}.log"
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target_intervals = "#{random}_target.intervals"
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realigned_bam = "#{random}_realigned.bam"
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recal_file = "#{random}_recal.csv"
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recal_bam = "#{random}_recal.bam"
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options[:account] = options[:project] if options[:account].empty?
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# BWA : First step mapping reads to reference
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BwaCaller.call_paired_end(options[:mutant_r1],
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options[:mutant_r2],
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bam_file,
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options[:index_prefix],
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log_file,
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options[:bwa],
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options[:samtools],
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job_prefix,
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options[:account],
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options[:debug])
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# Indexing
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bam_file = bam_file + ".bam"
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SamtoolsIndexing.call(bam_file,
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job_prefix,
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options[:account],
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options[:debug])
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# Realigne
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GatkCaller.prepare_realigne(log_file,
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options[:gatk],
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bam_file,
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options[:index_fa],
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target_intervals,
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job_prefix,
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options[:account],
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options[:debug])
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GatkCaller.realigne(log_file,
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options[:gatk],
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bam_file,
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options[:index_fa],
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target_intervals,
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realigned_bam,
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job_prefix,
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options[:account],
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options[:debug])
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# Recalibration
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GatkCaller.recalibrate_bam( log_file,
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options[:gatk],
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options[:index_fa],
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options[:index_vcf],
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realigned_bam,
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recal_file,
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job_prefix,
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options[:account],
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options[:debug] )
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GatkCaller.table_calibration(log_file,
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options[:gatk],
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options[:index_fa],
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realigned_bam,
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recal_bam,
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recal_file,
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job_prefix,
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options[:account],
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options[:debug])
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# GATK: finding mutations
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GatkCaller.call(log_file,
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options[:gatk],
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options[:index_fa],
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recal_bam,
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options[:vcf],
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job_prefix,
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options[:account],
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options[:debug])
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Binary file
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@@ -0,0 +1,18 @@
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1
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class BwaCaller
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def self.call_single_end(r1,out_file,index, log_file, bwa, samtools)
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cmd = "#{bwa} samse -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
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<(#{bwa} aln #{index} #{r1} 2>>#{log_file}) \
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|
+
#{r1} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"
|
6
|
+
puts cmd
|
7
|
+
system('bash','-c',cmd )
|
8
|
+
end
|
9
|
+
|
10
|
+
def self.call_paired_end(r1, r2, out_file, index, log_file, bwa, samtools, job_prefix,account, debug)
|
11
|
+
cmd = "qsub -cwd -b y -N #{job_prefix}_bwa -l h_vmem=9G -pe make 4 #{account}\
|
12
|
+
#{bwa} sampe -r '@RG\tID:foo\tSM:bar\tPL:Illumina' #{index} \
|
13
|
+
<(#{bwa} aln #{index} #{r1} 2>>#{log_file} || exit 1) <(#{bwa} aln #{index} #{r2} 2>>#{log_file} ) \
|
14
|
+
#{r1} #{r2} 2>>#{log_file} | #{samtools} view -Su - 2>>#{log_file} | #{samtools} sort - #{out_file} 2>>#{log_file}"
|
15
|
+
puts cmd
|
16
|
+
system('bash','-c', cmd) if debug == 1
|
17
|
+
end
|
18
|
+
end
|
@@ -0,0 +1,70 @@
|
|
1
|
+
class GatkCaller
|
2
|
+
# INDEX is normal genom.fa
|
3
|
+
# Genotyper
|
4
|
+
def self.call(log_dir, gatk, index_fa, read_bam, read_vcf, job_prefix, account, debug)
|
5
|
+
cmd = "echo 'starting GATK for mutant at ' `date` >> #{log_dir}
|
6
|
+
qsub -cwd -b y -N #{job_prefix}_genotyper -l h_vmem=3G -hold_jid #{job_prefix}_recalibration #{account}\
|
7
|
+
java -Xmx4g -jar #{gatk} -l INFO -R #{index_fa} -T UnifiedGenotyper \
|
8
|
+
-I #{read_bam} \
|
9
|
+
-o #{read_vcf} \
|
10
|
+
--genotype_likelihoods_model BOTH \
|
11
|
+
>> #{log_dir} 2>&1 || exit 1"
|
12
|
+
puts cmd
|
13
|
+
system(cmd) if debug == 1
|
14
|
+
end
|
15
|
+
|
16
|
+
# Making recalibration table
|
17
|
+
def self.recalibrate_bam(log_dir ,gatk, index_fa, index_vcf, read_bam, recal_file, job_prefix, account, debug )
|
18
|
+
cmd = "echo 'starting recalibration table ' `date` >> #{log_dir}
|
19
|
+
qsub -cwd -b y -N #{job_prefix}_recalibration_table -l h_vmem=3G #{account} \
|
20
|
+
java -Xmx4g -jar #{gatk} -knownSites #{index_vcf} -I #{read_bam} \
|
21
|
+
-R #{index_fa} -T CountCovariates \
|
22
|
+
-cov ReadGroupCovariate -cov QualityScoreCovariate -cov DinucCovariate \
|
23
|
+
-cov CycleCovariate \
|
24
|
+
-recalFile #{recal_file} >> #{log_dir} 2>&1 || exit 1 "
|
25
|
+
puts cmd
|
26
|
+
system(cmd) if debug == 1
|
27
|
+
end
|
28
|
+
|
29
|
+
# Using recalibration table
|
30
|
+
def self.table_calibration(log_dir, gatk, index_fa, read_bam, recal_bam, recal_file, job_prefix, account, debug)
|
31
|
+
cmd = "echo 'recalibrating bam_file at ' `date` >> #{log_dir}
|
32
|
+
qsub -cwd -b y -N #{job_prefix}_recalibration -l h_vmem=3G -hold_jid #{job_prefix}_recalibration_table #{account} \
|
33
|
+
java -Xmx4g -jar #{gatk} \
|
34
|
+
-R #{index_fa} \
|
35
|
+
-I #{read_bam} \
|
36
|
+
-T TableRecalibration \
|
37
|
+
-o #{recal_bam} \
|
38
|
+
-recalFile #{recal_file} >> #{log_dir} 2>&1 || exit 1"
|
39
|
+
puts cmd
|
40
|
+
system(cmd) if debug == 1
|
41
|
+
end
|
42
|
+
|
43
|
+
# Preparation realignement
|
44
|
+
def self.prepare_realigne(log_dir, gatk, read_bam, index_fa, target_intervals, job_prefix, account, debug)
|
45
|
+
cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
|
46
|
+
qsub -cwd -b y -N #{job_prefix}_prep_realignment -l h_vmem=3G -hold_jid #{job_prefix}_indexing #{account}\
|
47
|
+
java -Xmx2g -jar #{gatk} \
|
48
|
+
-I #{read_bam} \
|
49
|
+
-R #{index_fa} \
|
50
|
+
-T RealignerTargetCreator \
|
51
|
+
-o #{target_intervals}"
|
52
|
+
puts cmd
|
53
|
+
system(cmd) if debug == 1
|
54
|
+
end
|
55
|
+
|
56
|
+
# Realignment
|
57
|
+
def self.realigne(log_dir, gatk, read_bam, index_fa, target_intervals, realigned_bam, job_prefix, account, debug)
|
58
|
+
cmd = "echo 'preparing realignement at ' `date` >> #{log_dir}
|
59
|
+
qsub -cwd -b y -N #{job_prefix}_realignment -l h_vmem=3G -hold_jid #{job_prefix}_prep_realignment #{account} \
|
60
|
+
java -Xmx4g -jar #{gatk} \
|
61
|
+
-I #{read_bam} \
|
62
|
+
-R #{index_fa} \
|
63
|
+
-T IndelRealigner \
|
64
|
+
-targetIntervals #{target_intervals} \
|
65
|
+
-o #{realigned_bam} >> #{log_dir} 2>&1 || exit 1"
|
66
|
+
puts cmd
|
67
|
+
system(cmd) if debug == 1
|
68
|
+
end
|
69
|
+
|
70
|
+
end
|
@@ -0,0 +1,21 @@
|
|
1
|
+
class LocationFile
|
2
|
+
def self.create(vcf_file, loction_file_output)
|
3
|
+
locations = File.open(vcf_file)
|
4
|
+
line = locations.readline()
|
5
|
+
|
6
|
+
locus = []
|
7
|
+
while line.include?('#')
|
8
|
+
location = line.scan(/##contig=<ID=+\w+/)
|
9
|
+
if !location.empty?()
|
10
|
+
location = location[0].split('=')
|
11
|
+
locus << location[-1]
|
12
|
+
end
|
13
|
+
line = locations.readline()
|
14
|
+
end
|
15
|
+
|
16
|
+
locations.close()
|
17
|
+
locus_file = File.new(location_file_output,'w')
|
18
|
+
locus_file.write(locus.join("\n"))
|
19
|
+
locus_file.close()
|
20
|
+
end
|
21
|
+
end
|
metadata
ADDED
@@ -0,0 +1,56 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: mutations_caller_pipeline_aws
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.6
|
5
|
+
prerelease:
|
6
|
+
platform: ruby
|
7
|
+
authors:
|
8
|
+
- Kaharina Hayer
|
9
|
+
autorequire:
|
10
|
+
bindir: bin
|
11
|
+
cert_chain: []
|
12
|
+
date: 2012-01-20 00:00:00.000000000 Z
|
13
|
+
dependencies: []
|
14
|
+
description: Using BWA to align and GATK to call the bases
|
15
|
+
email:
|
16
|
+
- katharinaehayer@gmail.com
|
17
|
+
executables:
|
18
|
+
- mutations_caller_pipeline_aws
|
19
|
+
- gatk_pipe_only_aws
|
20
|
+
extensions: []
|
21
|
+
extra_rdoc_files: []
|
22
|
+
files:
|
23
|
+
- bin/gatk_pipe_only_aws
|
24
|
+
- bin/mutations_caller_pipeline_aws
|
25
|
+
- lib/mutations_caller_pipeline_aws.rb
|
26
|
+
- lib/mutations_caller_pipeline_aws/.DS_Store
|
27
|
+
- lib/mutations_caller_pipeline_aws/bwa_caller.rb
|
28
|
+
- lib/mutations_caller_pipeline_aws/gatk_caller.rb
|
29
|
+
- lib/mutations_caller_pipeline_aws/location_file.rb
|
30
|
+
- lib/mutations_caller_pipeline_aws/samtools_indexing.rb
|
31
|
+
homepage: https://github.com/khayer/mutations_caller_pipeline_aws
|
32
|
+
licenses: []
|
33
|
+
post_install_message:
|
34
|
+
rdoc_options: []
|
35
|
+
require_paths:
|
36
|
+
- lib
|
37
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
38
|
+
none: false
|
39
|
+
requirements:
|
40
|
+
- - ! '>='
|
41
|
+
- !ruby/object:Gem::Version
|
42
|
+
version: '0'
|
43
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
44
|
+
none: false
|
45
|
+
requirements:
|
46
|
+
- - ! '>='
|
47
|
+
- !ruby/object:Gem::Version
|
48
|
+
version: '0'
|
49
|
+
requirements: []
|
50
|
+
rubyforge_project: mutations_caller_pipeline_aws
|
51
|
+
rubygems_version: 1.8.10
|
52
|
+
signing_key:
|
53
|
+
specification_version: 3
|
54
|
+
summary: Call Mutations for files.fq
|
55
|
+
test_files: []
|
56
|
+
has_rdoc:
|