protk 1.1.5 → 1.1.7

data/lib/protk/constants.rb

@@ -216,6 +216,11 @@ class Constants
 
     @protk_dir="#{Dir.home}/.protk"
 
+    if ( ENV['PROTK_INSTALL_DIR']!=nil )
+      p "Using protk install dir from shell"
+      @protk_dir=ENV['PROTK_INSTALL_DIR']
+    end
+
 
     default_config_yml = YAML.load_file "#{File.dirname(__FILE__)}/data/default_config.yml"
     throw "Unable to read the config file at #{File.dirname(__FILE__)}/data/default_config.yml" unless default_config_yml!=nil

data/lib/protk/manage_db_rakefile.rake

@@ -445,8 +445,9 @@ end
 # Indexing        #
 ###################
 if dbspec[:make_blast_index] 
-  blast_index_files=FileList.new([".phr"].collect {|ext| "#{db_filename}#{ext}"  })
+#  blast_index_files=FileList.new([".phr"].collect {|ext| "#{db_filename}#{ext}"  })
   #  task :make_blast_index => blast_index_files  do
+  blast_index_files=["#{db_filename}.phr"]
   blast_index_files.each do |indfile|
     file indfile => db_filename do
       cmd="cd #{dbdir}; #{$genv.makeblastdb} -in #{db_filename} -parse_seqids -dbtype prot"

data/lib/protk/setup_rakefile.rake

@@ -101,7 +101,7 @@ file perl_locallib_installed_file =>  [@build_dir,"#{@download_dir}/#{perl_local
 	sh %{cp #{@download_dir}/#{perl_locallib_packagefile} #{@build_dir}}
 	perl_dir = "#{env.protk_dir}/perl5"
 
-	sh %{cd #{@build_dir}; gunzip local-lib-#{perl_locallib_version}.tar.gz } 
+	sh %{cd #{@build_dir}; gunzip -f local-lib-#{perl_locallib_version}.tar.gz } 
 	sh %{cd #{@build_dir}; tar -xf local-lib-#{perl_locallib_version}.tar } 
 	sh "cd #{@build_dir}/local-lib-#{perl_locallib_version}; perl Makefile.PL --bootstrap=#{perl_dir}; make install" do |ok,res|
 #		clean_build_dir if ok
@@ -330,8 +330,11 @@ file protk_galaxy_envfile do
 	sh %{cp #{this_dir}/data/galaxyenv.sh #{protk_galaxy_envfile}}
 end
 
-task :galaxy => protk_galaxy_envfile
+task :galaxyenv => protk_galaxy_envfile
 
-task :all => [:tpp,:omssa,:blast,:msgfplus,:pwiz,:openms,:galaxy]
+task :all => [:tpp,:omssa,:blast,:msgfplus,:pwiz,:openms,:galaxyenv]
 
+# Special task when installing via toolshed
+#
+task :galaxy => [:tpp,:omssa,:blast,:pwiz,:galaxyenv]
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.1.5
+  version: 1.1.7
   prerelease: 
 platform: ruby
 authors: