From c796b25c1a70217a7f542bda4a7a51efb66f5b86 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 17 Nov 2009 13:49:00 +0100 Subject: Passenger (re)start fixed --- Rakefile | 5 +- bin/opentox-install-debian.sh | 105 +++++++++++++++++++++++++++++++++++++++ lib/tasks/opentox.rb | 16 ++---- opentox-ruby-api-wrapper.gemspec | 20 ++++++-- 4 files changed, 129 insertions(+), 17 deletions(-) create mode 100644 bin/opentox-install-debian.sh diff --git a/Rakefile b/Rakefile index 2c4322f..9d042a5 100644 --- a/Rakefile +++ b/Rakefile @@ -15,10 +15,13 @@ begin gem.add_dependency "rack" gem.add_dependency "rack-contrib" gem.add_dependency "thin" - gem.add_dependency "cucumber" gem.add_dependency "ezmobius-redis-rb" gem.add_dependency "emk-sinatra-url-for" gem.add_dependency "cehoffman-sinatra-respond_to" + gem.add_dependency "dm-core" + gem.add_dependency "datamapper" + gem.add_dependency "do_sqlite3" + gem.add_development_dependency "cucumber" gem.files = FileList["[A-Z]*", "{bin,generators,lib,test}/**/*", 'lib/jeweler/templates/.gitignore'] gem.files.include %w(lib/tasks/opentox.rb, lib/tasks/redis.rb, lib/environment.rb, lib/algorithm.rb, lib/compound.rb, lib/dataset.rb, lib/feature.rb, lib/model.rb, lib/utils.rb, lib/templates/*) # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings diff --git a/bin/opentox-install-debian.sh b/bin/opentox-install-debian.sh new file mode 100644 index 0000000..cf173da --- /dev/null +++ b/bin/opentox-install-debian.sh @@ -0,0 +1,105 @@ +#!/bin/bash +#Installation is tested on Debian Lenny Ubuntu 9.04 +#Update the system + +ERRLOG='install_err.log' +INSTALLLOG='install_log.log' +DATE=$(date +%Y/%m/%d\ %H:%M:%S) + +echo "=================================================" +echo "Please enshure that the sudo package is installed" +echo "on your system. " +echo "On Ubuntu Linux sudo is installed by default." +echo "If you are unshure check with it 'sudo ls'" +echo "and installed it with 'apt-get install sudo'" +echo "and add your username with visudo." +echo "=================================================" +echo -n "To continue installation press y: " +read answer +if [ "$answer" != "y" ] +then + echo "exiting the script..." + exit 1 +fi + +echo "opentox webservice install log - " $DATE > $INSTALLLOG +echo "Installing: build-essential" +sudo apt-get install build-essential >> $INSTALLLOG 2>>$ERRLOG +echo "Installing: ruby 1.8 with its dev files" +sudo apt-get install ruby ruby1.8-dev >> $INSTALLLOG 2>>$ERRLOG +echo "Installing: gems rdoc rubygems and rake" +sudo apt-get install gems rdoc rubygems rake >> $INSTALLLOG 2>>$ERRLOG + +echo "Installing rubygems from source. This may take some time" +wget http://rubyforge.org/frs/download.php/60718/rubygems-1.3.5.tgz >> $INSTALLLOG 2>>$ERRLOG +tar xzfv rubygems-1.3.5.tgz 2>>$ERRLOG +cd rubygems-1.3.5 >> $INSTALLLOG 2>>$ERRLOG +sudo ruby setup.rb 2>>$ERRLOG +cd .. + +echo "Adding http://gems.github.com to ruby gem sources" +sudo gem sources -a http://gems.github.com >> $INSTALLLOG 2>>$ERRLOG + +#for debian lenny: +echo "Installing packages: zlib1g-dev tcl curl perl ssh tcl tk8.5" +sudo apt-get install zlib1g-dev tcl curl perl ssh tcl tk8.5 >> $INSTALLLOG 2>>$ERRLOG +echo "Installing git from source" +wget http://www.kernel.org/pub/software/scm/git/git-1.6.5.2.tar.gz >> $INSTALLLOG 2>>$ERRLOG +tar xzfv git-1.6.5.2.tar.gz 2>>$ERRLOG +cd git-1.6.5.2 >> $INSTALLLOG 2>>$ERRLOG +./configure 2>>$ERRLOG +make 2>>$ERRLOG +make install 2>>$ERRLOG + +echo "Installing the opentox webservices" +mkdir webservices >> $INSTALLLOG 2>>$ERRLOG +cd webservices >> $INSTALLLOG 2>>$ERRLOG + +git clone git://github.com/helma/opentox-compound.git >> $INSTALLLOG 2>>$ERRLOG +git clone git://github.com/helma/opentox-feature.git >> $INSTALLLOG 2>>$ERRLOG +git clone git://github.com/helma/opentox-dataset.git >> $INSTALLLOG 2>>$ERRLOG +git clone git://github.com/helma/opentox-algorithm.git >> $INSTALLLOG 2>>$ERRLOG +git clone git://github.com/helma/opentox-model.git >> $INSTALLLOG 2>>$ERRLOG +git clone git://github.com/helma/opentox-test.git >> $INSTALLLOG 2>>$ERRLOG + +cd opentox-compound >> $INSTALLLOG 2>>$ERRLOG +git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG +cd ../opentox-feature >> $INSTALLLOG 2>>$ERRLOG +git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG +cd ../opentox-dataset >> $INSTALLLOG 2>>$ERRLOG +git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG +cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG +git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG +cd ../opentox-model >> $INSTALLLOG 2>>$ERRLOG +git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG +cd .. >> $INSTALLLOG 2>>$ERRLOG +git clone git://github.com/helma/opentox-ruby-api-wrapper.git >> $INSTALLLOG 2>>$ERRLOG +cd opentox-ruby-api-wrapper >> $INSTALLLOG 2>>$ERRLOG +git checkout -b development origin/development >> $INSTALLLOG 2>>$ERRLOG +rake install >> $INSTALLLOG 2>>$ERRLOG + + +cd ../opentox-compound >> $INSTALLLOG 2>>$ERRLOG +echo "Installing libopenssl-ruby" +sudo apt-get install libopenssl-ruby >> $INSTALLLOG 2>>$ERRLOG +echo "Installing dtach" +rake dtach:install >> $INSTALLLOG 2>>$ERRLOG +echo "Installing openbabel" +rake openbabel:install >> $INSTALLLOG 2>>$ERRLOG + +#debian lenny missed liblink: +ln -s /usr/local/lib/libopenbabel.so.3 /usr/lib/libopenbabel.so.3 >> $INSTALLLOG 2>>$ERRLOG + +rake redis:download >> $INSTALLLOG 2>>$ERRLOG +rake redis:install >> $INSTALLLOG 2>>$ERRLOG +#edit /home/[username]/.opentox/config/test.yaml set :base_dir: /home/[username]/webservices +sudo apt-get install libgsl0-dev >> $INSTALLLOG 2>>$ERRLOG +sudo apt-get install swig >> $INSTALLLOG 2>>$ERRLOG +sudo apt-get install curl >> $INSTALLLOG 2>>$ERRLOG +cd ../opentox-algorithm >> $INSTALLLOG 2>>$ERRLOG +echo "Installing fminer" +rake fminer:install >> $INSTALLLOG 2>>$ERRLOG +sudo apt-get install libsqlite3-dev >> $INSTALLLOG 2>>$ERRLOG + + +mkdir ../opentox-model/db >> $INSTALLLOG 2>>$ERRLOG diff --git a/lib/tasks/opentox.rb b/lib/tasks/opentox.rb index 8018fff..38202dd 100644 --- a/lib/tasks/opentox.rb +++ b/lib/tasks/opentox.rb @@ -22,16 +22,6 @@ end namespace :opentox do - desc "Install required gems" - task :install do - puts `sudo gem install #{@gems}` - end - - desc "Update gems" - task :update do - puts `sudo gem update #{@gems}` - end - namespace :services do desc "Run opentox services" @@ -51,7 +41,8 @@ namespace :opentox do puts "Cannot start #{service} on port #{port}." end when 'passenger' - `touch #{File.join(dir, 'tmp/restart.txt')}` + FileUtils.mkdir_p File.join(dir, 'tmp') + FileUtils.touch File.join(dir, 'tmp/restart.txt') puts "#{service} restarted." else puts "not yet implemented" @@ -108,7 +99,8 @@ task :start do puts "Cannot start #{service} on port #{port}." end when 'passenger' - `touch tmp/restart.txt` + FileUtils.mkdir_p File.join(dir, 'tmp') + FileUtils.touch File.join(dir, 'tmp/restart.txt') puts "#{service} restarted." else puts "not yet implemented" diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec index 17be199..c5b293d 100644 --- a/opentox-ruby-api-wrapper.gemspec +++ b/opentox-ruby-api-wrapper.gemspec @@ -5,13 +5,15 @@ Gem::Specification.new do |s| s.name = %q{opentox-ruby-api-wrapper} - s.version = "1.1.1" + s.version = "1.1.2" s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= s.authors = ["Christoph Helma"] s.date = %q{2009-11-17} + s.default_executable = %q{opentox-install-debian.sh} s.description = %q{Ruby wrapper for the OpenTox REST API (http://www.opentox.org)} s.email = %q{helma@in-silico.ch} + s.executables = ["opentox-install-debian.sh"] s.extra_rdoc_files = [ "LICENSE", "README.rdoc" @@ -21,6 +23,7 @@ Gem::Specification.new do |s| "README.rdoc", "Rakefile", "VERSION", + "bin/opentox-install-debian.sh", "lib/algorithm.rb", "lib/compound.rb", "lib/dataset.rb", @@ -56,20 +59,26 @@ Gem::Specification.new do |s| s.add_runtime_dependency(%q, [">= 0"]) s.add_runtime_dependency(%q, [">= 0"]) s.add_runtime_dependency(%q, [">= 0"]) - s.add_runtime_dependency(%q, [">= 0"]) s.add_runtime_dependency(%q, [">= 0"]) s.add_runtime_dependency(%q, [">= 0"]) s.add_runtime_dependency(%q, [">= 0"]) + s.add_runtime_dependency(%q, [">= 0"]) + s.add_runtime_dependency(%q, [">= 0"]) + s.add_runtime_dependency(%q, [">= 0"]) + s.add_development_dependency(%q, [">= 0"]) else s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) - s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) end else s.add_dependency(%q, [">= 0"]) @@ -77,9 +86,12 @@ Gem::Specification.new do |s| s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) - s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) + s.add_dependency(%q, [">= 0"]) end end -- cgit v1.2.3