bio-pipengine 0.6.0

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Files changed (11) hide show
  1. checksums.yaml +7 -0
  2. data/LICENSE.txt +20 -0
  3. data/README.md +631 -0
  4. data/VERSION +1 -0
  5. data/bin/pipengine +101 -0
  6. data/lib/bio/pipengine/job.rb +271 -0
  7. data/lib/bio/pipengine/sample.rb +13 -0
  8. data/lib/bio/pipengine/step.rb +39 -0
  9. data/lib/bio/pipengine.rb +234 -0
  10. data/lib/bio-pipengine.rb +13 -0
  11. metadata +167 -0
data/lib/bio-pipengine.rb ADDED
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+ require 'yaml'
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+
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+ require 'securerandom'
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+ require 'trollop'
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+ require 'colorize'
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+ require 'torque_rm'
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+ require 'terminal-table'
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+ require 'fileutils'
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+
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+ require 'bio/pipengine/sample'
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+ require 'bio/pipengine/step'
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+ require 'bio/pipengine/job'
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+ require 'bio/pipengine'
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-pipengine
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+ version: !ruby/object:Gem::Version
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+ version: 0.6.0
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+ platform: ruby
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+ authors:
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+ - Francesco Strozzi
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2015-03-26 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: trollop
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: colorize
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: torque_rm
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: terminal-table
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: shoulda
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">"
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">"
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 1.8.4
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: 1.8.4
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+ description: A pipeline manager
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+ email: francesco.strozzi@gmail.com
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+ executables:
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+ - pipengine
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+ extensions: []
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+ extra_rdoc_files:
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+ - LICENSE.txt
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+ - README.md
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+ files:
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+ - LICENSE.txt
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+ - README.md
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+ - VERSION
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+ - bin/pipengine
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+ - lib/bio-pipengine.rb
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+ - lib/bio/pipengine.rb
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+ - lib/bio/pipengine/job.rb
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+ - lib/bio/pipengine/sample.rb
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+ - lib/bio/pipengine/step.rb
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+ homepage: http://github.com/fstrozzi/bioruby-pipengine
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+ licenses:
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+ - MIT
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 2.2.2
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+ signing_key:
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+ specification_version: 4
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+ summary: A pipeline manager
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+ test_files: []