protk 1.1.9 → 1.1.10

data/lib/protk/constants.rb

@@ -244,7 +244,7 @@ class Constants
     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
+      dict = user_config_yml.merge dict 
     end
 
     File.open("#{self.protk_dir}/config.yml", "w") {|file| file.puts(dict.to_yaml) }

data/lib/protk/data/apt-get_packages.yaml

@@ -10,9 +10,6 @@ rvm:
 - openssl
 - libreadline6
 - libreadline6-dev
-- openssl
-- libreadline6
-- libreadline6-dev
 - git-core
 - zlib1g
 - zlib1g-dev
@@ -26,11 +23,14 @@ rvm:
 - subversion
 - pkg-config
 
+protk:
+- libxml2-dev
+- libxml2
+
 galaxy:
 - mercurial
 
 tpp:
-- cpanminus
 - g++
 - subversion
 - libbz2-dev

data/lib/protk/setup_rakefile.rake

@@ -34,9 +34,12 @@ def download_buildfile url, file
 end
 
 def download_task url, packagefile
-	file "#{@download_dir}/#{packagefile}" => @download_dir do 
+	file "#{@download_dir}/#{packagefile}" => @download_dir do
+		p "Downloading from #{url}"
 		download_buildfile "#{url}", "#{packagefile}"
+		p "Done"
 	end
+	"#{@download_dir}/#{packagefile}"
 end
 
 #
@@ -94,12 +97,13 @@ perl_locallib_version="1.008004"
 perl_locallib_packagefile="local-lib-#{perl_locallib_version}.tar.gz"
 perl_locallib_installed_file = "#{env.protk_dir}/perl5/lib/perl5/local/lib.pm"
 perl_locallib_url = "http://search.cpan.org/CPAN/authors/id/A/AP/APEIRON/local-lib-#{perl_locallib_version}.tar.gz"
+perl_dir = "#{env.protk_dir}/perl5"
 
 download_task perl_locallib_url, perl_locallib_packagefile
 
 file perl_locallib_installed_file =>  [@build_dir,"#{@download_dir}/#{perl_locallib_packagefile}"] do
 	sh %{cp #{@download_dir}/#{perl_locallib_packagefile} #{@build_dir}}
-	perl_dir = "#{env.protk_dir}/perl5"
+	
 
 	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 } 
@@ -107,13 +111,13 @@ file perl_locallib_installed_file =>  [@build_dir,"#{@download_dir}/#{perl_local
 #		clean_build_dir if ok
 	end
 
-	if !Pathname.new("~/.bashrc").exist? || File.read("~/.bashrc") =~ /Mlocal::lib/
-		sh "echo 'eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir})' >>~/.bashrc"
-	end
+	# if !Pathname.new("~/.bashrc").exist? || File.read("~/.bashrc") =~ /Mlocal::lib/
+	# 	sh "echo 'eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir})' >>~/.bashrc"
+	# end
 
-	if !Pathname.new("~/.bash_profile").exist? || File.read("~/.bash_profile") =~ /Mlocal::lib/
-		sh "echo 'eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir})' >>~/.bash_profile"
-	end
+	# if !Pathname.new("~/.bash_profile").exist? || File.read("~/.bash_profile") =~ /Mlocal::lib/
+	# 	sh "echo 'eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir})' >>~/.bash_profile"
+	# end
 
 	sh "eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});curl -L http://cpanmin.us | perl - --self-upgrade"
 end
@@ -134,13 +138,13 @@ tpp_packagefile="TPP-#{tpp_version}.tgz"
 tpp_installed_file = "#{env.xinteract}"
 tpp_url = "https://dl.dropbox.com/u/226794/TPP-4.6.1.tgz"
 
-download_task tpp_url, tpp_packagefile
+tpp_download_file = download_task tpp_url, tpp_packagefile
 
 # Build
-file tpp_installed_file => [:perl_locallib,@build_dir,"#{@download_dir}/#{tpp_packagefile}"] do
+file tpp_installed_file => [:perl_locallib,@build_dir,tpp_download_file] do
 	sh %{cp #{@download_dir}/#{tpp_packagefile} #{@build_dir}}
-	sh %{cpanm --local-lib=#{env.protk_dir}/perl5 XML::Parser}
-	sh %{cpanm --local-lib=#{env.protk_dir}/perl5 CGI --force}
+	sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cpanm --local-lib=#{env.protk_dir}/perl5 XML::Parser}
+	sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cpanm --local-lib=#{env.protk_dir}/perl5 CGI --force}
 
 	sh %{cd #{@build_dir};tar -xvzf TPP-#{tpp_version}.tgz}
 
@@ -168,7 +172,7 @@ file tpp_installed_file => [:perl_locallib,@build_dir,"#{@download_dir}/#{tpp_pa
 			f.write subs_text
 		end
 	end
-	sh %{cd #{@build_dir}/TPP-#{tpp_version}/trans_proteomic_pipeline/src ; make; make install}
+	sh %{eval $(perl -I#{perl_dir}/lib/perl5 -Mlocal::lib=#{perl_dir});cd #{@build_dir}/TPP-#{tpp_version}/trans_proteomic_pipeline/src ; make; make install}
 
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: protk
 version: !ruby/object:Gem::Version
-  version: 1.1.9
+  version: 1.1.10
   prerelease: 
 platform: ruby
 authors: