sushi_fabric 0.5.9 → 0.6.0
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- checksums.yaml +7 -0
- data/README.md +19 -2
- data/lib/sushi_fabric/sushiApp.rb +2 -2
- data/lib/sushi_fabric/version.rb +1 -1
- metadata +51 -51
checksums.yaml
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SHA1:
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metadata.gz: 06c6576ae298fa353b6a918ff6eebee9219f1504
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data/README.md
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# SushiFabric
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This library includes a core process called from [SUSHI](https://github.com/uzh/sushi). sushi_fabric command becomes available after installation. It requires [WorkflowManager](https://github.com/uzh/workflow_manager) to execute sushi_fabric command. SUSHI application must inherit the SushiFabric:SushiApp class and overwrite #next_dataset and #commands methods. Please refer to [SUSHI](https://github.com/uzh/sushi) for more details about how to make SUSHI application.
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## Installation
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@@ -18,7 +18,24 @@ Or install it yourself as:
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## Usage
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-
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~~~~
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$ sushi_fabric -h 16-05-10 15:37
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Usage:
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sushi_fabric --class [SushiApp class] [options]
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(Either --dataset_id or --dataset_tsv is required)
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-c, --class class_name SushiApp class name (required)
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-i, --dataset_id dataset_id DataSet ID in Sushi DB
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-d, --dataset dataset_tsv DataSet file (.tsv) (This option is prior to dataset_id option)
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-s, --dataset_name dataset_name DataSet name in Sushi (This will be used with --dataset option, default: tsv file base name)
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-m parameterset_tsv, Parameterset file (.tsv)
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--parameterset
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-r, --run Real run mode. without this option, it runs with test run mode which checks only DataSet and Parameters and no submittion
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-p, --project project Project Number (default: 1001)
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-u, --user user Submit user (default: sushi_lover)
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-I, --load_path load_path Add path where SushiApp class is located (default: ./lib)
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-n next_dataset_name, Next DataSet Name (default: Analysis_Category+ID+Date )
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--next_dataset_name
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~~~~
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## Contributing
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#!/usr/bin/env ruby
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# encoding: utf-8
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# Version = '
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# Version = '20160715-153019'
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require 'csv'
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require 'fileutils'
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require 'yaml'
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require 'drb/drb'
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gem 'rails'
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gem 'rails'
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require 'rails/all'
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module SushiFabric
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data/lib/sushi_fabric/version.rb
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metadata
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@@ -1,51 +1,54 @@
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--- !ruby/object:Gem::Specification
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--- !ruby/object:Gem::Specification
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name: sushi_fabric
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version: !ruby/object:Gem::Version
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version: 0.5.9
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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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authors:
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- Functional Genomics Center Zurich
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autorequire:
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bindir: bin
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cert_chain: []
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-
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-
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-
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- !ruby/object:Gem::Dependency
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date: 2016-07-15 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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-
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-
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-
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-
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-
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- !ruby/object:Gem::Version
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version: "1.3"
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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: '1.3'
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type: :development
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version_requirements: *id001
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- !ruby/object:Gem::Dependency
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name: rake
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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: '1.3'
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- !ruby/object:Gem::Dependency
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name: rake
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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:
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- !ruby/object:Gem::Version
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version: '0'
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type: :development
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-
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-
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-
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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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description: This library provides us with the methods to submit a job cooperating
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with workflow manager.
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email:
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- masaomi.hatakeyama@fgcz.uzh.ch
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executables:
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executables:
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- sushi_fabric
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extensions: []
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-
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extra_rdoc_files: []
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-
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-
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- .
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- .rspec
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files:
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- ".gitignore"
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- ".rspec"
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- Gemfile
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- LICENSE.txt
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- README.md
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@@ -62,33 +65,30 @@ files:
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- spec/spec_helper.rb
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- spec/sushi_app_spec.rb
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- sushi_fabric.gemspec
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homepage:
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licenses:
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homepage: ''
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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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-
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require_paths:
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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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-
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requirements:
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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:
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required_rubygems_version: !ruby/object:Gem::Requirement
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requirements:
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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:
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- !ruby/object:Gem::Version
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version: '0'
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requirements: []
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-
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rubyforge_project:
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rubygems_version:
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rubygems_version: 2.4.5.1
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signing_key:
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specification_version:
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specification_version: 4
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summary: workflow manager client.
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test_files:
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test_files:
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- spec/spec_helper.rb
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- spec/sushi_app_spec.rb
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