rbbt-image 0.1.0

checksums.yaml

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data/README.md

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+# Vagrant file for Rbbt
+
+## Instructions
+
+* Install [Vagrant](http://www.vagrantup.com)
+* Clone repo
+* `vagrant up`
+
+To retrieve special provisions for apps etc. check the branches. You may use
+the `bin/build_provision_sh` to build a provision script that you can use in
+Docker (see example)
+
+```bash
+bin/build_provision_sh -w Translation,Sequence > mydocker_image/provision.sh
+cp Dockerfile mydocker_image/
+docker build -t <repo:tag> mydocker_image/
+```
+
+The `bin/build_provision_sh` script is documented, try the `-h` flag for
+options, these include options for specifying which workflows to bootstrap, or 
+configuring remote servers for resources and for workflows.

data/bin/build_rbbt_provision_sh.rb

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+#!/usr/bin/env ruby
+# -*- mode: ruby -*-
+# vi: set ft=ruby :
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+require 'rbbt/util/cmd'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Build a provision script
+
+$ #{$0} [options]
+
+-h--help Print this help
+-u--user* System user to bootstrap
+-w--workflow* Workflows to bootstrap (has defaults specify 'none' to avoid them)
+-s--server* Main Rbbt remote server (file-server and workflow server)
+-fs--file_server* Rbbt remote file server
+-ws--workflow_server* Rbbt remote workflow server
+-rr--remote_resources* Remote resources to gather from file-server
+-rw--remote_workflows* Remote workflows server from workflow-server
+-ss--skip_base_system Skip base system installation
+-sr--skip_ruby Skip ruby setup installation
+-su--skip_user_setup Skip user setup
+-sb--skip_bootstrap Skip user bootstrap
+-c--concurrent Prepare system for high-concurrency
+-dt--docker* Build docker image using the provided name
+-df--docker_file* Use a Dockerfile different than the default
+-dd--docker_dependency* Use a different image in the Dockerfile FROM
+EOF
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage and exit 0 
+  else
+    puts SOPT.doc
+    exit
+  end
+end
+
+USER = options[:user] || 'rbbt'
+SKIP_BASE_SYSTEM = options[:skip_base_system]
+SKIP_RUBY = options[:skip_ruby]
+SKIP_BOOT = options[:skip_bootstrap]
+SKIP_USER = options[:skip_user_setup]
+
+VARIABLES={
+ :RBBT_LOG => 0,
+ :BOOTSTRAP_WORKFLOWS => (options[:workflow] || "Enrichment Translation Sequence MutationEnrichment").split(/[\s,]+/)*" ",
+ :REMOTE_RESOURCES => (options[:remote_resources] || "KEGG").split(/[\s,]+/)*" "
+}
+
+VARIABLES[:BOOTSTRAP_WORKFLOWS] = "" if VARIABLES[:BOOTSTRAP_WORKFLOWS] == 'none'
+
+VARIABLES[:RBBT_NO_LOCKFILE_ID] = "true" if options[:concurrent]
+VARIABLES[:RBBT_SERVER] = options[:server] if options[:server]
+VARIABLES[:RBBT_FILE_SERVER] = options[:file_server] if options[:file_server]
+VARIABLES[:RBBT_WORKFLOW_SERVER] = options[:workflow_server] if options[:workflow_server]
+VARIABLES[:REMOTE_WORKFLOWS] = options[:remote_workflows].split(/[\s,]+/)*" " if options[:remote_workflows]
+
+
+provision_script =<<EOF
+cat "$0"
+echo "Running provisioning"
+echo
+
+
+# BASE SYSTEM
+echo "1. Provisioning base system"
+#{File.read("share/provision_scripts/ubuntu_setup.sh") unless SKIP_BASE_SYSTEM}
+
+# BASE SYSTEM
+echo "2. Setting up ruby"
+#{File.read("share/provision_scripts/ruby_setup.sh") unless SKIP_RUBY}
+
+#{"exit" if SKIP_USER}
+
+####################
+# USER CONFIGURATION
+
+if [[ '#{ USER }' == 'root' ]] ; then
+  home_dir='/root'
+else
+  useradd -ms /bin/bash #{USER}
+  home_dir='/home/#{USER}'
+fi
+
+user_script=$home_dir/.rbbt/bin/provision
+mkdir -p $(dirname $user_script)
+chown -R #{USER} /home/#{USER}/.rbbt/
+cat > $user_script <<'EUSER'
+
+. /etc/profile
+
+echo "2.1. Custom variables"
+#{
+  VARIABLES.collect do |variable,value|
+    "export " << ([variable,'"' << value.to_s << '"'] * "=")
+  end * "\n"
+}
+
+echo "2.2. Default variables"
+#{ File.read("share/provision_scripts/variables.sh") }
+
+echo "2.3. Configuring rbbt"
+#{File.read("share/provision_scripts/user_setup.sh")}
+
+#{"exit" if SKIP_BOOT}
+
+echo "2.4. Bootstrap system"
+#{File.read("share/provision_scripts/bootstrap.sh")}
+
+EUSER
+####################
+echo "2. Running user configuration as '#{USER}'"
+chown #{USER} $user_script;
+su -l -c "bash $user_script" #{USER}
+
+# DONE
+echo
+echo "Installation done."
+
+#--------------------------------------------------------
+
+EOF
+
+docker_dependency = options[:docker_dependency]
+
+if options[:docker]
+  dockerfile = options[:dockerfile] || File.join(File.dirname(File.dirname(__FILE__)), 'Dockerfile')
+  dockerfile_text = Open.read(dockerfile)
+  dockerfile_text.sub!(/^FROM.*/,'FROM ' + docker_dependency) if docker_dependency
+  TmpFile.with_file(nil, false) do |dir|
+    FileUtils.mkdir_p dir
+    Path.setup(dir)
+    Open.write(dir["Dockerfile"].find, dockerfile_text)
+    Open.write(dir['provision.sh'], provision_script)
+
+    puts
+    puts "provision.sh"
+    puts "=========="
+    puts provision_script
+
+    puts
+    puts "Dockerfile"
+    puts "=========="
+    puts dockerfile_text
+
+    puts
+    puts "RUN"
+    puts "=========="
+    puts "docker build -t #{options[:docker]} '#{dir}'"
+    io = CMD.cmd("docker build -t #{options[:docker]} '#{dir}'", :pipe => true, :log => true)
+    while line = io.gets
+      puts line
+    end
+  end
+else
+  puts provision_script
+end
+

data/bin/run_rbbt_docker.rb

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+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+
+Runs a docker image from an infrastructure definition file
+
+$ #{ $0 } [options] <infrastructure.yaml> <command> <args>
+
+Infrastruture definition comes in YAML
+
+-h--help Print this help
+
+EOF
+infrastructure_file, cmd, *cmd_args = ARGV
+
+cmd_args.collect!{|a| "'" << a << "'" }
+
+if options[:help] or infrastructure_file.nil?
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.usage
+  end
+  exit 0
+end
+
+
+infrastructure = File.open(infrastructure_file){|io| YAML.load io }
+IndiferentHash.setup(infrastructure)
+
+image = infrastructure[:image]
+
+if user = infrastructure[:user]
+  user_conf = "-u #{user} -e HOME=/home/#{user}/ "
+else
+  user_conf = ""
+end
+
+mount_conf = ""
+if infrastructure[:mounts]
+  infrastructure[:mounts].each do |target,source|
+    target = target.gsub("USER", user)
+    if source.nil? or source.empty?
+      mount_conf << " -v #{target}"
+    else
+      mount_conf << " -v #{File.expand_path(source)}:#{target}"
+    end
+  end
+end
+
+if infrastructure[:workflow_autoinstall] and infrastructure[:workflow_autoinstall].to_s == 'true'
+  cmd = "env RBBT_WORKFLOW_AUTOINSTALL=true " + cmd
+end
+
+cmd_str = "docker run #{mount_conf} #{user_conf} #{image} #{cmd} #{cmd_args*" "} "
+Log.info "Running docker: \n" << cmd_str
+Log.severity = 0
+io = CMD.cmd(cmd_str, :pipe => true, :log => true, :stderr => 0)
+
+while line = io.gets
+  puts line
+end
+

metadata

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+--- !ruby/object:Gem::Specification
+name: rbbt-image
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Miguel Vazquez
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-10-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rbbt-util
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Builds provision files for docker and Vagrant and helps run them
+email: miguel.vazquez@cnio.es
+executables:
+- build_rbbt_provision_sh.rb
+- run_rbbt_docker.rb
+extensions: []
+extra_rdoc_files:
+- README.md
+files:
+- README.md
+- bin/build_rbbt_provision_sh.rb
+- bin/run_rbbt_docker.rb
+homepage: http://github.com/mikisvaz/rbbt-image
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.6
+signing_key: 
+specification_version: 4
+summary: Build docker and Vagrant (VM) images
+test_files: []