protk 1.1.7 → 1.1.8

data/bin/feature_finder.rb

@@ -72,7 +72,7 @@ ARGV.each do |filen|
   if ( tool.over_write || !Pathname.new(output_file).exist? )
     output_base_filename=Pathname.new(output_file).basename.to_s
     cmd=""
-    cmd<<"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.protk/tools/openms/lib;
+    cmd<<"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:#{genv.openms_root}/lib;
 #{genv.featurefinderisotopewavelet} -in #{Pathname.new(input_file).realpath.to_s} -out #{output_dir}/#{output_base_filename} -ini #{ini_file}"
   
     run_ff(genv,tool,cmd,output_file,tool.jobid_from_filename(input_basename))

data/bin/protk_setup.rb

@@ -6,8 +6,19 @@
 # Post-install setup for protk. 
 # Installs third party tools
 #
-
 require 'protk/constants'
+
+toolname=ARGV[0]
+
+if ARGV[1]=='--change-location'
+	location=ARGV[2]
+	p "Changing default location for #{toolname} to #{location}"
+	env=Constants.new
+	env.update_user_config({"#{toolname}_root"=>location})
+	exit
+end
+
+
 require 'protk/setup_tool'
 require 'yaml'
 require 'pp'
@@ -26,28 +37,12 @@ if ( ARGV.length < 1)
 	exit
 end
 
-# Checking for required options
-# begin
-#   tool.option_parser.parse!
-#   mandatory = [:gff_predicted, :protxml,:sixframe] 
-#   missing = mandatory.select{ |param| tool.send(param).nil? }
-#   if not missing.empty?                                            
-#     puts "Missing options: #{missing.join(', ')}"                  
-#     puts tool.option_parser                                                  
-#     exit                                                           
-#   end                                                              
-# rescue OptionParser::InvalidOption, OptionParser::MissingArgument      
-#   puts $!.to_s                                                           
-#   puts tool.option_parser                                              
-#   exit                                                                   
-# end
-
-
-# Create install directory if it doesn't already exist
-#
 env=Constants.new
 
-ARGV.each do |toolname|
-	p toolname
-	tool.install toolname
-end
+toolname=ARGV.shift
+
+p ARGV
+p toolname
+
+p "Installing #{toolname}"
+tool.install toolname

data/bin/toppas_pipeline.rb

@@ -66,7 +66,7 @@ trf_path = "#{tool.toppas_file}.trf"
 generate_trf(ARGV,trf_path)
 
 cmd=""
-cmd<<"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/.protk/tools/openms/lib;
+cmd<<"export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:#{genv.openms_root}/lib;
 #{genv.executepipeline} -in #{Pathname.new(tool.toppas_file).realpath.to_s} -out_dir #{Pathname.new(tool.outdir).realpath.to_s} -resource_file #{Pathname.new(trf_path).realpath.to_s}"
 
 run_pipeline(genv,tool,cmd,tool.outdir,tool.jobid_from_filename(tool.toppas_file))

data/lib/protk/constants.rb

@@ -240,6 +240,16 @@ class Constants
     
   end
 
+  def update_user_config(dict)
+    user_config_yml = YAML.load_file "#{self.protk_dir}/config.yml" if File.exist? "#{self.protk_dir}/config.yml"
+
+    if ( user_config_yml !=nil )
+      dict = dict.merge user_config_yml
+    end
+
+    File.open("#{self.protk_dir}/config.yml", "w") {|file| file.puts(dict.to_yaml) }
+
+  end
 
   def initialize_loggers
     log_dir = Pathname.new(self.log_file).dirname

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.1.7
+  version: 1.1.8
   prerelease: 
 platform: ruby
 authors: