protk 1.2.6.pre3 → 1.2.6.pre4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: 39ba2f20593785f7a9720be1d48fa1e37f694b22
+  metadata.gz: f779db7583731b118880ba56e4c465b0a75856a3
+  data.tar.gz: 459bfa1d39a6c8b11d6b04f4c2c30a0b85115f30
 SHA512:
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-  data.tar.gz: f61d8418f78b958d2b586c2a2f975fc6caf6b0ef4bb9838a5a9c7f5f7b90f22e96b6210cef3b27c91f038aa0764089481318cfe7f71793726c77e80f379b3705
+  metadata.gz: 340df071b94a8658354e08d2c30a642cd1d715d2312b9e0eec7c67fd6be36a16ab77430cdf4160cb0365d53f747c3af7471168af39a0afdbc7c761801f853671
+  data.tar.gz: 2e19a8b4ecd4af37077157f1eafbcb4d9dc7850b135e55853199ffd7637f417e264459fec0818fc298854d96afae96a53e2f0b5f2454e9b2c8898bdfd51612a1

data/bin/interprophet.rb

@@ -12,6 +12,7 @@ require 'protk/command_runner'
 require 'protk/prophet_tool'
 require 'protk/galaxy_util'
 
+for_galaxy = GalaxyUtil.for_galaxy?
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
@@ -72,13 +73,13 @@ if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
   cmd << " MINPROB=#{prophet_tool.min_prob}" if ( prophet_tool.min_prob !="" )
 
   inputs = ARGV.collect {|file_name| 
-    input_name=file_name.chomp
-    unless input_name !~/pep\.xml$/
-        input_name = GalaxyStager.new(input_name, :extension => ".pep.xml").staged_path
-    end
-    input_name
+    file_name.chomp
   }
 
+  if for_galaxy
+    inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
+  end
+
   cmd << " #{inputs.join(" ")} #{output_file}"
 
   genv.log("Running #{cmd}",:info)

data/bin/msgfplus_search.rb

@@ -104,6 +104,8 @@ genv=Constants.new
 #
 msgf_bin="#{genv.msgfplusjar}"
 
+throw "Could not find MSGFPlus.jar" if (msgf_bin==nil) || (msgf_bin.length==0)
+
 make_msgfdb_cmd=""
 
 case 

data/bin/peptide_prophet.rb

@@ -12,7 +12,8 @@ require 'protk/command_runner'
 require 'protk/prophet_tool'
 require 'protk/galaxy_util'
 
-galaxy_util = GalaxyUtil.new
+for_galaxy = GalaxyUtil.for_galaxy?
+input_stager = nil
 
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
@@ -120,15 +121,15 @@ genv=Constants.new
 
 
 inputs=ARGV.collect { |file_name| file_name.chomp}
-if galaxy_util.for_galaxy? 
-  inputs = inputs.collect {|ip| galaxy_util.stage_pepxml(ip) }
+if for_galaxy
+  inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
 end
 
 # Interrogate all the input files to obtain the database and search engine from them
 #
 genv.log("Determining search engine and database used to create input files ...",:info)
 file_info={}
-ARGV.each {|file_name| 
+inputs.each {|file_name| 
   name=file_name.chomp
   
   engine=prophet_tool.extract_engine(name)
@@ -167,7 +168,7 @@ end
 
 def generate_command(genv,prophet_tool,inputs,output,database,engine)
   
-  cmd="#{genv.xinteract} -N#{output}  -l7 -eT -D'#{database}' "
+  cmd="xinteract -N#{output}  -l7 -eT -D'#{database}' "
 
   if prophet_tool.glyco 
     cmd << " -Og "

data/bin/protein_prophet.rb

@@ -15,15 +15,6 @@ require 'protk/galaxy_util'
 
 for_galaxy = GalaxyUtil.for_galaxy?
 
-if for_galaxy
-  # Stage files for galaxy
-  original_input_file = ARGV[0]
-  original_input_path = Pathname.new("#{original_input_file}")
-  input_stager = GalaxyStager.new("#{original_input_file}", :extension => '.pep.xml')
-  ARGV.push("-o")
-  ARGV.push("protein_prophet_results.prot.xml")  
-end
-
 # Setup specific command-line options for this tool. Other options are inherited from ProphetTool
 #
 prophet_tool=ProphetTool.new([:glyco,:explicit_output,:over_write,:prefix_suffix])
@@ -112,12 +103,17 @@ p output_file
 
 if ( !Pathname.new(output_file).exist? || prophet_tool.over_write )
 
-  cmd="#{genv.proteinprophet} "
+  cmd="ProteinProphet "
 
   inputs = ARGV.collect {|file_name| 
     file_name.chomp
   }
 
+  if for_galaxy
+    inputs = inputs.collect {|ip| GalaxyUtil.stage_pepxml(ip) }
+  end
+
+
   cmd << " #{inputs.join(" ")} #{output_file}"
 
   if ( prophet_tool.glyco )

data/lib/protk/constants.rb

@@ -35,7 +35,9 @@ class Constants
   # This will be used for all constants other than paths
   #
   def method_missing(method)
-    @env[method.to_s]
+    from_env = @env[method.to_s]
+    throw "#{method} is undefined" unless from_env!=nil
+    from_env
   end
 
   # Some constants are paths. They need to be translated into real paths before being returned
@@ -46,137 +48,33 @@ class Constants
   end
   
   def tpp_root
-    path=@env['tpp_root']
-    if ( path =~ /^\// )
-      return path
-    else
-      return "#{@protk_dir}/#{@env['tpp_root']}"
-    end
-  end
-
-  def xinteract
-    return "#{self.tpp_root}/bin/xinteract"
-  end
-
-  def xtandem    
-    return "#{self.tpp_root}/bin/tandem"
-  end
-
-  def tandem2xml
-    return "#{self.tpp_root}/bin/Tandem2XML"
-  end
-  
-  def interprophetparser
-    return "#{self.tpp_root}/bin/InterProphetParser"
-  end
-
-  def proteinprophet
-    return "#{self.tpp_root}/bin/ProteinProphet"
-  end
-
-  def asapratiopeptideparser
-    return "#{self.tpp_root}/bin/ASAPRatioPeptideParser"
+      "#{@protk_dir}/tools/tpp"
   end
 
-  def asapratioproteinparser
-    return "#{self.tpp_root}/bin/ASAPRatioProteinRatioParser"
-  end
-
-  def asaprationpvalueparser
-    return "#{self.tpp_root}/bin/ASAPRatioPvalueParser"
-  end
-
-  def librapeptideparser
-    return "#{self.tpp_root}/bin/LibraPeptideParser"
-  end
-
-  def libraproteinratioparser
-    return "#{self.tpp_root}/bin/LibraProteinRatioParser"
-  end
-
-  def xpresspeptideparser
-    return "#{self.tpp_root}/bin/XPressPeptideParser"
-  end
-
-  def xpressproteinratioparser
-    return "#{self.tpp_root}/bin/XPressProteinRatioParser"
-  end
-
-  def mascot2xml
-    return "#{self.tpp_root}/bin/Mascot2XML"
-  end
   
   def omssa_root
-    path=@env['omssa_root']
-    if ( path =~ /^\// )
-      return path
-    else
-      return "#{@protk_dir}/#{@env['omssa_root']}"
-    end
-  end
-
-  def omssacl
-    return "#{self.omssa_root}/omssacl"
-  end
-
-  def omssa2pepxml
-    return "#{self.omssa_root}/omssa2pepXML"
+      "#{@protk_dir}/tools/omssa"
   end
   
   def msgfplus_root
-    path=@env['msgfplus_root']
-    if ( path =~ /^\// )
-      return path
-    else
-      return "#{@protk_dir}/#{@env['msgfplus_root']}"
-    end
+    "#{@protk_dir}/tools/msgfplus"
   end
 
   def msgfplusjar
-    return %x[which MSGFPlus.jar]
+    msgfplus_path=%x[which MSGFPlus.jar]
+    msgfplus_path.chomp
   end
 
   def pwiz_root
-    path=@env['pwiz_root']
-    if ( path =~ /^\// )
-      return path
-    else
-      return "#{@protk_dir}/#{@env['pwiz_root']}"
-    end    
-  end
-
-  def msconvert
-    return "#{self.pwiz_root}/msconvert"
+      return "#{@protk_dir}/tools/pwiz"
   end
 
   def openms_root
-    path=@env['openms_root']
-    if ( path =~ /^\//)
-      return path 
-    else
-      return "#{@protk_dir}/#{@env['openms_root']}"
-    end
-  end
-
-  def featurefinderisotopewavelet
-    return "#{self.openms_root}/bin/FeatureFinderIsotopeWavelet"
-  end
-
-  def executepipeline
-    return "#{self.openms_root}/bin/ExecutePipeline"
+      "#{@protk_dir}/tools/openms"
   end
 
   def tandem_root
-    path=@env['tandem_root']
-    if ( path =~ /^\//)
-      return path 
-    else
-      return "#{@protk_dir}/#{@env['tandem_root']}"
-    end
-  end
-
-  def gpmtandem
-    return "#{self.tandem_root}/bin/tandem"
+      "#{@protk_dir}/tools/tandem"
   end
 
   def protein_database_root
@@ -193,20 +91,7 @@ class Constants
   end
   
   def blast_root
-    path=@env['blast_root']
-    if ( path =~ /^\// )
-      return path
-    else
-      return "#{@protk_dir}/#{@env['blast_root']}"   
-    end 
-  end
-
-  def makeblastdb
-    return "makeblastdb"
-  end
-
-  def searchblastdb
-    return "#{self.blast_root}/bin/blastdbcmd"
+      "#{@protk_dir}/blast"   
   end
   
   def log_file
@@ -247,7 +132,7 @@ class Constants
       @env=default_config_yml
     end
 
-    protk_tool_dirs=["tpp","omssa","openms","msgfplus","blast","pwiz","tandem"]
+    protk_tool_dirs=["tpp/bin","omssa","openms/bin","msgfplus","blast/bin","pwiz","tandem/bin"]
 
     # Construct the PATH variable by prepending our preferred paths
     #

data/lib/protk/galaxy_stager.rb

@@ -15,8 +15,8 @@ class GalaxyStager
     @staged_path = "#{@staged_base}#{@extension}"
     if options[:force_copy]
       FileUtils.copy(@original_path, @staged_path)
-    else
-      File.symlink(@original_path, @staged_path)
+    else      
+      File.symlink(@original_path, @staged_path) unless File.symlink?@staged_path
     end
   end
 

data/lib/protk/galaxy_util.rb

@@ -6,18 +6,14 @@ require 'fileutils'
 
 class GalaxyUtil
 
-  attr_accessor :for_galaxy
-  attr_accessor :stagers
-
-  def initialize()
-    @for_galaxy= ARGV[0]=="--galaxy"
-    ARGV.shift if @for_galaxy    
-    @stagers=[]
+  def self.for_galaxy?    
+    fg = ARGV[0]=="--galaxy"
+    ARGV.shift if fg
+    fg
   end
 
-  def stage_pepxml(input_pepxml_path)
+  def self.stage_pepxml(input_pepxml_path)
     stager = GalaxyStager.new(input_pepxml_path, :extension => ".pep.xml")
-    @stagers << stager
     stager.staged_path
   end
 

data/lib/protk/setup_rakefile.rake

@@ -133,10 +133,10 @@ task :perl_locallib => [perl_locallib_installed_file]
 #
 # TPP
 #
-tpp_version="4.6.2"
+tpp_version="4.6.3"
 tpp_packagefile="TPP-#{tpp_version}.tgz"
-tpp_installed_file = "#{env.xinteract}"
-tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.2.tgz"
+tpp_installed_file = "#{env.tpp_root}/bin/xinteract"
+tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.3.tgz"
 
 tpp_download_file = download_task tpp_url, tpp_packagefile
 
@@ -198,7 +198,7 @@ def omssa_platform
 end
 
 omssa_packagefile="omssa-#{omssa_platform}.tar.gz"
-omssa_installed_file = "#{env.omssacl}"
+omssa_installed_file = "#{env.omssa_root}/omssacl"
 omssa_url = "ftp://ftp.ncbi.nih.gov/pub/lewisg/omssa/CURRENT/omssa-#{omssa_platform}.tar.gz"
 
 download_task omssa_url, omssa_packagefile
@@ -229,7 +229,7 @@ end
 blast_version="2.2.27+"
 blast_packagefile="ncbi-blast-#{blast_version}-#{blast_platform}.tar.gz"
 blast_url="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/#{blast_version.chomp('+')}/#{blast_packagefile}"
-blast_installed_file="#{env.makeblastdb}"
+blast_installed_file="#{env.blast_root}/bin/makeblastdb"
 
 download_task blast_url, blast_packagefile
 
@@ -248,10 +248,10 @@ task :blast => blast_installed_file
 #
 # MSGFPlus
 #
-msgfplus_version="20130410"
+msgfplus_version="20140210"
 msgfplus_packagefile="MSGFPlus.#{msgfplus_version}.zip"
-msgfplus_url="http://proteomics.ucsd.edu/Downloads/MSGFPlus.#{msgfplus_version}.zip"
-msgfplus_installed_file="#{env.msgfplusjar}"
+msgfplus_url="http://proteomics.ucsd.edu/Software/MSGFPlus/MSGFPlus.#{msgfplus_version}.zip"
+msgfplus_installed_file="#{env.msgfplus_root}/MSGFPlus.jar"
 
 download_task msgfplus_url, msgfplus_packagefile
 
@@ -285,7 +285,7 @@ pwiz_version="3_0_4388"
 pwiz_folder_name="pwiz-bin-#{pwiz_platform}-release-#{pwiz_version}"
 pwiz_packagefile="#{pwiz_folder_name}.tar.bz2"
 pwiz_url="https://dl.dropbox.com/u/226794/#{pwiz_packagefile}"
-pwiz_installed_file="#{env.idconvert}"
+pwiz_installed_file="#{env.pwiz_root}/idconvert"
 
 download_task pwiz_url, pwiz_packagefile
 
@@ -313,7 +313,7 @@ end
 openms_version="1.10.0"
 openms_packagefile="OpenMS-#{openms_version}.tar.gz"
 openms_url="https://dl.dropbox.com/u/226794/#{openms_packagefile}"
-openms_installed_file="#{env.featurefinderisotopewavelet}"
+openms_installed_file="#{env.openms_root}/bin/FileConverter"
 
 download_task openms_url, openms_packagefile
 
@@ -340,10 +340,10 @@ def tandem_platform
 	'linux'
 end
 
-tandem_version="13-02-01-1"
+tandem_version="13-09-01-1"
 tandem_packagefile="tandem-#{tandem_platform}-#{tandem_version}.zip"
-tandem_url="ftp://ftp.thegpm.org/projects/tandem/source/#{tandem_packagefile}"
-tandem_installed_file="#{env.gpmxtandem}"
+tandem_url="https://dl.dropboxusercontent.com/u/226794/galaxy/#{tandem_packagefile}"
+tandem_installed_file="#{env.tandem_root}/bin/tandem.exe"
 
 download_task tandem_url, tandem_packagefile
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.2.6.pre3
+  version: 1.2.6.pre4
 platform: ruby
 authors:
 - Ira Cooke