protk 1.1.11 → 1.1.12

data/lib/protk/constants.rb

@@ -232,6 +232,16 @@ class Constants
     else
       @env=default_config_yml
     end
+
+    protk_roots = ["tpp","omssa","blast","pwiz","msgfplus","openms"]
+
+    protk_roots.each do |r|  
+      env_value = ENV["PROTK_#{r.upcase}_ROOT"]
+      if ( env_value!=nil)
+        p "Using #{r} root #{env_value}"
+        @env["#{r}_root"]=env_value
+      end
+    end
     
     throw "No data found in config file" unless @env!=nil
     @info_level=default_config_yml['message_level']
@@ -240,6 +250,7 @@ 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"
 

data/lib/protk/setup_rakefile.rake

@@ -274,7 +274,7 @@ def platform_bunzip
 	'bunzip2'
 end
 
-pwiz_version="3_0_4146"
+pwiz_version="3_0_4388"
 pwiz_packagefile="pwiz-bin-#{pwiz_platform}-release-#{pwiz_version}.tar.bz2"
 pwiz_url="https://dl.dropbox.com/u/226794/#{pwiz_packagefile}"
 pwiz_installed_file="#{env.idconvert}"
@@ -286,7 +286,7 @@ file pwiz_installed_file => [@build_dir,"#{@download_dir}/#{pwiz_packagefile}"]
     sh %{cd #{@build_dir}; #{platform_bunzip} -f #{pwiz_packagefile}}
     sh %{cd #{@build_dir}; tar -xvf #{pwiz_packagefile.chomp('.bz2')}}
     sh %{mkdir -p #{env.pwiz_root}}
-    sh %{cd #{@build_dir}; cp idconvert msconvert #{env.pwiz_root}/}
+    sh %{cd #{@build_dir}; cp chainsaw idconvert msaccess mscat msdiff msistats peakaboo pepsum txt2mzml idcat msbenchmark msconvert msdir mspicture pepcat sldout unimod_2.xsd license #{env.pwiz_root}/}
 end
 
 task :pwiz => pwiz_installed_file

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.1.11
+  version: 1.1.12
   prerelease: 
 platform: ruby
 authors: