mspire-simulator 0.1.1 → 0.1.2

data/README.rdoc

@@ -7,7 +7,7 @@ Description:
   gem install mspire-simulator
 Dependencies:
   ruby 1.9*
-  weka 3.6.0
+  weka 3.6.0 - May need to add to CLASSPATH see: http://weka.wikispaces.com/CLASSPATH+problems
   fftw 3.2.2 - Tested in Linux Mint 12 and Ubuntu Oneiric Ocelot
 == Examples
  

data/Rakefile

@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
   gem.add_dependency "obo", "= 0.1.0"
   gem.add_dependency "trollop", "= 1.16.2"
   
-  gem.executables = ["mspire-simulator"]
+  gem.executables = ["mspire-simulator","sim_mail"]
   gem.files.exclude "elution_curvefit.svg"
   gem.files.exclude "intensity_var_curvefit.svg"
   gem.files.exclude "lib/pool.rb"

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/bin/mspire-simulator

@@ -120,8 +120,8 @@ module MspireSimulator
     end
     puts "Exception - Simulation Failed"
     
-    system "ruby bin/sim_mail.rb #{email} Exception - Simulation Failed" if email != "nil"
+    system "sim_mail #{email} Exception - Simulation Failed" if email != "nil"
   else
-    system "ruby bin/sim_mail.rb #{email} Success! - Simulation Complete" if email != "nil"
+    system "sim_mail #{email} Success! - Simulation Complete" if email != "nil"
   end
 end

data/lib/ms/rt/weka.rb

@@ -13,7 +13,10 @@ module MS
         data<<pep.aa_counts
       end
       arff = make_rt_arff(Time.now.nsec.to_s,data)
-      system("java weka.classifiers.functions.MultilayerPerceptron -T #{arff} -l bin/weka/M5Rules.model -p 24 > #{arff}.out")
+      
+      path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
+      dir = path[0..path.size-3].join("/")
+      system("java weka.classifiers.functions.MultilayerPerceptron -T #{arff} -l #{dir}/lib/weka/M5Rules.model -p 24 > #{arff}.out")
       system("rm #{arff}")
       
       #extract what was predicted by weka model
@@ -39,7 +42,10 @@ module MS
         data << array.concat(pep.aa_counts)
       end
       arff = make_int_arff(Time.now.nsec.to_s,data)
-      system("java weka.classifiers.trees.M5P -T #{arff} -l bin/weka/M5P.model -p 27 > #{arff}.out")
+      
+      path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
+      dir = path[0..path.size-3].join("/")
+      system("java weka.classifiers.trees.M5P -T #{arff} -l #{dir}/lib/weka/M5P.model -p 27 > #{arff}.out")
       system("rm #{arff}")
       
       #extract what was predicted by weka model

data/mspire-simulator.gemspec

@@ -5,14 +5,14 @@
 
 Gem::Specification.new do |s|
   s.name = "mspire-simulator"
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["anoyce"]
   s.date = "2012-08-10"
   s.description = "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.\n\t\t\tCan simulate specific data if given an MZML file containing a single isolated peptide peak."
   s.email = "andrewbnoyce@gmail.com"
-  s.executables = ["mspire-simulator"]
+  s.executables = ["mspire-simulator", "sim_mail"]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -23,10 +23,7 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "bin/mspire-simulator",
-    "bin/sim_mail.rb",
-    "bin/weka/M5P.model",
-    "bin/weka/M5Rules.model",
-    "bin/weka/weka.jar",
+    "bin/sim_mail",
     "lib/ms/curvefit.rb",
     "lib/ms/curvefit/curve_fit_helper.rb",
     "lib/ms/curvefit/fit_graph.rb",
@@ -45,6 +42,8 @@ Gem::Specification.new do |s|
     "lib/ms/sim_trollop.rb",
     "lib/ms/tr_file_writer.rb",
     "lib/progress.rb",
+    "lib/weka/M5P.model",
+    "lib/weka/M5Rules.model",
     "mspire-simulator.gemspec",
     "spec/file_writer_spec.rb",
     "spec/merger_spec.rb",

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire-simulator
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -177,6 +177,7 @@ description: ! "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML
 email: andrewbnoyce@gmail.com
 executables:
 - mspire-simulator
+- sim_mail
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
@@ -187,10 +188,7 @@ files:
 - Rakefile
 - VERSION
 - bin/mspire-simulator
-- bin/sim_mail.rb
-- bin/weka/M5P.model
-- bin/weka/M5Rules.model
-- bin/weka/weka.jar
+- bin/sim_mail
 - lib/ms/curvefit.rb
 - lib/ms/curvefit/curve_fit_helper.rb
 - lib/ms/curvefit/fit_graph.rb
@@ -209,6 +207,8 @@ files:
 - lib/ms/sim_trollop.rb
 - lib/ms/tr_file_writer.rb
 - lib/progress.rb
+- lib/weka/M5P.model
+- lib/weka/M5Rules.model
 - mspire-simulator.gemspec
 - spec/file_writer_spec.rb
 - spec/merger_spec.rb