protk 1.2.6.pre3 → 1.2.6.pre4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/bin/interprophet.rb +6 -5
- data/bin/msgfplus_search.rb +2 -0
- data/bin/peptide_prophet.rb +6 -5
- data/bin/protein_prophet.rb +6 -10
- data/lib/protk/constants.rb +13 -128
- data/lib/protk/galaxy_stager.rb +2 -2
- data/lib/protk/galaxy_util.rb +5 -9
- data/lib/protk/setup_rakefile.rake +13 -13
- metadata +1 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: f779db7583731b118880ba56e4c465b0a75856a3
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data.tar.gz: 459bfa1d39a6c8b11d6b04f4c2c30a0b85115f30
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 340df071b94a8658354e08d2c30a642cd1d715d2312b9e0eec7c67fd6be36a16ab77430cdf4160cb0365d53f747c3af7471168af39a0afdbc7c761801f853671
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data.tar.gz: 2e19a8b4ecd4af37077157f1eafbcb4d9dc7850b135e55853199ffd7637f417e264459fec0818fc298854d96afae96a53e2f0b5f2454e9b2c8898bdfd51612a1
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data/bin/interprophet.rb
CHANGED
@@ -12,6 +12,7 @@ require 'protk/command_runner'
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require 'protk/prophet_tool'
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require 'protk/galaxy_util'
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for_galaxy = GalaxyUtil.for_galaxy?
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# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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#
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@@ -72,13 +73,13 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
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cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
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inputs = ARGV.collect {|file_name|
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unless input_name !~/pep\.xml$/
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input_name = GalaxyStager.new(input_name, :extension => ".pep.xml").staged_path
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end
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input_name
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file_name.chomp
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}
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if for_galaxy
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inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
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end
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cmd << " #{inputs.join(" ")} #{output_file}"
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genv.log("Running #{cmd}",:info)
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data/bin/msgfplus_search.rb
CHANGED
data/bin/peptide_prophet.rb
CHANGED
@@ -12,7 +12,8 @@ require 'protk/command_runner'
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require 'protk/prophet_tool'
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require 'protk/galaxy_util'
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for_galaxy = GalaxyUtil.for_galaxy?
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input_stager = nil
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# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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#
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@@ -120,15 +121,15 @@ genv=Constants.new
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inputs=ARGV.collect { |file_name| file_name.chomp}
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if
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inputs = inputs.collect {|ip|
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if for_galaxy
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inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
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end
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# Interrogate all the input files to obtain the database and search engine from them
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#
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genv.log("Determining search engine and database used to create input files ...",:info)
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file_info={}
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-
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inputs.each {|file_name|
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name=file_name.chomp
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engine=prophet_tool.extract_engine(name)
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@@ -167,7 +168,7 @@ end
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def generate_command(genv,prophet_tool,inputs,output,database,engine)
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cmd="
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cmd="xinteract -N#{output} -l7 -eT -D'#{database}' "
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if prophet_tool.glyco
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cmd << " -Og "
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data/bin/protein_prophet.rb
CHANGED
@@ -15,15 +15,6 @@ require 'protk/galaxy_util'
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for_galaxy = GalaxyUtil.for_galaxy?
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if for_galaxy
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# Stage files for galaxy
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original_input_file = ARGV[0]
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original_input_path = Pathname.new("#{original_input_file}")
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input_stager = GalaxyStager.new("#{original_input_file}", :extension => '.pep.xml')
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ARGV.push("-o")
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ARGV.push("protein_prophet_results.prot.xml")
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end
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# Setup specific command-line options for this tool. Other options are inherited from ProphetTool
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#
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prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix_suffix])
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@@ -112,12 +103,17 @@ p output_file
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if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
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cmd="
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cmd="ProteinProphet "
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inputs = ARGV.collect {|file_name|
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file_name.chomp
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}
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if for_galaxy
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inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
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end
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cmd << " #{inputs.join(" ")} #{output_file}"
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if ( prophet_tool.glyco )
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data/lib/protk/constants.rb
CHANGED
@@ -35,7 +35,9 @@ class Constants
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# This will be used for all constants other than paths
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#
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def method_missing(method)
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@env[method.to_s]
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from_env = @env[method.to_s]
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throw "#{method} is undefined" unless from_env!=nil
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from_env
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end
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# Some constants are paths. They need to be translated into real paths before being returned
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end
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def tpp_root
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if ( path =~ /^\// )
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return path
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else
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return "#{@protk_dir}/#{@env['tpp_root']}"
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end
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end
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def xinteract
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return "#{self.tpp_root}/bin/xinteract"
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end
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def xtandem
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return "#{self.tpp_root}/bin/tandem"
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end
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def tandem2xml
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return "#{self.tpp_root}/bin/Tandem2XML"
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end
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def interprophetparser
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return "#{self.tpp_root}/bin/InterProphetParser"
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end
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def proteinprophet
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return "#{self.tpp_root}/bin/ProteinProphet"
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end
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def asapratiopeptideparser
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return "#{self.tpp_root}/bin/ASAPRatioPeptideParser"
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"#{@protk_dir}/tools/tpp"
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end
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def asapratioproteinparser
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return "#{self.tpp_root}/bin/ASAPRatioProteinRatioParser"
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end
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def asaprationpvalueparser
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return "#{self.tpp_root}/bin/ASAPRatioPvalueParser"
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end
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def librapeptideparser
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return "#{self.tpp_root}/bin/LibraPeptideParser"
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end
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def libraproteinratioparser
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return "#{self.tpp_root}/bin/LibraProteinRatioParser"
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end
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def xpresspeptideparser
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return "#{self.tpp_root}/bin/XPressPeptideParser"
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end
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def xpressproteinratioparser
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return "#{self.tpp_root}/bin/XPressProteinRatioParser"
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end
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def mascot2xml
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return "#{self.tpp_root}/bin/Mascot2XML"
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end
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def omssa_root
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if ( path =~ /^\// )
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return path
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else
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return "#{@protk_dir}/#{@env['omssa_root']}"
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end
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end
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def omssacl
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return "#{self.omssa_root}/omssacl"
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end
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def omssa2pepxml
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return "#{self.omssa_root}/omssa2pepXML"
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"#{@protk_dir}/tools/omssa"
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end
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def msgfplus_root
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if ( path =~ /^\// )
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return path
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else
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return "#{@protk_dir}/#{@env['msgfplus_root']}"
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end
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"#{@protk_dir}/tools/msgfplus"
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end
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def msgfplusjar
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msgfplus_path=%x[which MSGFPlus.jar]
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msgfplus_path.chomp
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end
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def pwiz_root
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if ( path =~ /^\// )
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return path
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else
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return "#{@protk_dir}/#{@env['pwiz_root']}"
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end
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end
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def msconvert
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return "#{self.pwiz_root}/msconvert"
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return "#{@protk_dir}/tools/pwiz"
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end
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def openms_root
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if ( path =~ /^\//)
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return path
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else
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return "#{@protk_dir}/#{@env['openms_root']}"
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end
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end
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def featurefinderisotopewavelet
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return "#{self.openms_root}/bin/FeatureFinderIsotopeWavelet"
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end
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def executepipeline
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return "#{self.openms_root}/bin/ExecutePipeline"
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"#{@protk_dir}/tools/openms"
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end
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def tandem_root
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if ( path =~ /^\//)
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return path
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else
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return "#{@protk_dir}/#{@env['tandem_root']}"
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end
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end
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def gpmtandem
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return "#{self.tandem_root}/bin/tandem"
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"#{@protk_dir}/tools/tandem"
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end
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def protein_database_root
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@@ -193,20 +91,7 @@ class Constants
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end
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def blast_root
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if ( path =~ /^\// )
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return path
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else
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return "#{@protk_dir}/#{@env['blast_root']}"
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end
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end
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def makeblastdb
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return "makeblastdb"
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end
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def searchblastdb
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return "#{self.blast_root}/bin/blastdbcmd"
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"#{@protk_dir}/blast"
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end
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def log_file
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@@ -247,7 +132,7 @@ class Constants
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@env=default_config_yml
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end
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protk_tool_dirs=["tpp","omssa","openms","msgfplus","blast","pwiz","tandem"]
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protk_tool_dirs=["tpp/bin","omssa","openms/bin","msgfplus","blast/bin","pwiz","tandem/bin"]
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# Construct the PATH variable by prepending our preferred paths
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#
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data/lib/protk/galaxy_stager.rb
CHANGED
@@ -15,8 +15,8 @@ class GalaxyStager
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@staged_path = "#{@staged_base}#{@extension}"
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if options[:force_copy]
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FileUtils.copy(@original_path, @staged_path)
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else
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File.symlink(@original_path, @staged_path)
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else
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File.symlink(@original_path, @staged_path) unless File.symlink?@staged_path
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end
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end
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data/lib/protk/galaxy_util.rb
CHANGED
@@ -6,18 +6,14 @@ require 'fileutils'
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class GalaxyUtil
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@for_galaxy= ARGV[0]=="--galaxy"
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ARGV.shift if @for_galaxy
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@stagers=[]
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def self.for_galaxy?
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fg = ARGV[0]=="--galaxy"
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ARGV.shift if fg
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fg
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end
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def stage_pepxml(input_pepxml_path)
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def self.stage_pepxml(input_pepxml_path)
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stager = GalaxyStager.new(input_pepxml_path, :extension => ".pep.xml")
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@stagers << stager
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stager.staged_path
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end
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@@ -133,10 +133,10 @@ task :perl_locallib => [perl_locallib_installed_file]
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#
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# TPP
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#
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tpp_version="4.6.
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tpp_version="4.6.3"
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tpp_packagefile="TPP-#{tpp_version}.tgz"
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tpp_installed_file = "#{env.xinteract
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tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.
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tpp_installed_file = "#{env.tpp_root}/bin/xinteract"
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tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz"
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tpp_download_file = download_task tpp_url, tpp_packagefile
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@@ -198,7 +198,7 @@ def omssa_platform
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end
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omssa_packagefile="omssa-#{omssa_platform}.tar.gz"
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omssa_installed_file = "#{env.omssacl
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omssa_installed_file = "#{env.omssa_root}/omssacl"
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omssa_url = "ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/CURRENT/omssa-#{omssa_platform}.tar.gz"
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download_task omssa_url, omssa_packagefile
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@@ -229,7 +229,7 @@ end
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blast_version="2.2.27+"
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blast_packagefile="ncbi-blast-#{blast_version}-#{blast_platform}.tar.gz"
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blast_url="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/#{blast_version.chomp('+')}/#{blast_packagefile}"
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-
blast_installed_file="#{env.makeblastdb
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blast_installed_file="#{env.blast_root}/bin/makeblastdb"
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234
234
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download_task blast_url, blast_packagefile
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@@ -248,10 +248,10 @@ task :blast => blast_installed_file
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#
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# MSGFPlus
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#
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-
msgfplus_version="
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+
msgfplus_version="20140210"
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msgfplus_packagefile="MSGFPlus.#{msgfplus_version}.zip"
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-
msgfplus_url="http://proteomics.ucsd.edu/
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-
msgfplus_installed_file="#{env.
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+
msgfplus_url="http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.#{msgfplus_version}.zip"
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+
msgfplus_installed_file="#{env.msgfplus_root}/MSGFPlus.jar"
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download_task msgfplus_url, msgfplus_packagefile
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@@ -285,7 +285,7 @@ pwiz_version="3_0_4388"
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pwiz_folder_name="pwiz-bin-#{pwiz_platform}-release-#{pwiz_version}"
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pwiz_packagefile="#{pwiz_folder_name}.tar.bz2"
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pwiz_url="https://dl.dropbox.com/u/226794/#{pwiz_packagefile}"
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-
pwiz_installed_file="#{env.idconvert
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+
pwiz_installed_file="#{env.pwiz_root}/idconvert"
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download_task pwiz_url, pwiz_packagefile
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@@ -313,7 +313,7 @@ end
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openms_version="1.10.0"
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openms_packagefile="OpenMS-#{openms_version}.tar.gz"
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openms_url="https://dl.dropbox.com/u/226794/#{openms_packagefile}"
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-
openms_installed_file="#{env.
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+
openms_installed_file="#{env.openms_root}/bin/FileConverter"
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download_task openms_url, openms_packagefile
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@@ -340,10 +340,10 @@ def tandem_platform
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'linux'
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end
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-
tandem_version="13-
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+
tandem_version="13-09-01-1"
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tandem_packagefile="tandem-#{tandem_platform}-#{tandem_version}.zip"
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-
tandem_url="
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-
tandem_installed_file="#{env.
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+
tandem_url="https://dl.dropboxusercontent.com/u/226794/galaxy/#{tandem_packagefile}"
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+
tandem_installed_file="#{env.tandem_root}/bin/tandem.exe"
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download_task tandem_url, tandem_packagefile
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