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BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package
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Biogem provides a set of tools for those Bioinformaticans who want to start coding an application, or a library for using/extending BioRuby's core library and sharing the code as a gem through Biogems are automatically listed at

The basic idea is to promote a modular approach to the BioRuby package, and simplify creating such modules. Biogem creates the necessary directory structure for a gem, and generates files, based on templates. Biogem includes templates for parsing the command line, logging, libraries, documentation, tests. Also there is Ruby on Rails support, BioSQL and FFI (for binding to C libraries).

Biogem does not reinvent the wheel, but puts together different tools and modifies their original behavior, when needed. The tool jeweler is used to create the initial scaffold, setting up git for versioning, releasing it to and/or and packaging. Bundler is used used for setting up a predefined developing environment.

Also Biogem makes use of webservices. E.g.

  • and are two different services and you need to create different accounts for them if you already use you are set for using Biogem

Biogems Official Archive

Biogem Tutorial

The latest version is on

Contributing to Biogem

The source code repositories for Biogem and website are on github. If you want to contribute, feel free! Clone the project!


Toshiaki Katayama wrote a step by step guide for a bio-foobar plugin @

BioRuby's Wiki Official Documentation

Biogem options

Usage: biogem [options] reponame

e.g. biogem the-perfect-gem

--directory [DIRECTORY]      specify the directory to generate into

These options are for BioGem

–meta create a meta package, just the Rakefile, Gemfile, Licence, Readme. This options takes the precedence over every other option.

--with-bin                   create the bin directory and an executable template script called bioreponame
--with-db                    create the database directory for a db application-library.
--with-test-data             create the data directory inside the test directory if the user need to set up a test with its own dataset
--with-engine [NAMESPACE]    create a Rails engine with the namespace given in input. Set default database creation

These options are for Jeweler

    --rspec                      generate rspec code examples
    --shoulda                    generate shoulda tests
    --testunit                   generate test/unit tests
    --bacon                      generate bacon specifications
    --testspec                   generate test/spec tests
    --minitest                   generate minitest tests
    --micronaut                  generate micronaut examples
    --riot                       generate riot tests
    --shindo                     generate shindo tests

    --[no-]bundler               use bundler for managing dependencies
    --cucumber                   generate cucumber stories in addition to the other tests

    --reek                       generate rake task for reek
    --roodi                      generate rake task for roodi

    --summary [SUMMARY]          specify the summary of the project
    --description [DESCRIPTION]  specify a description of the project

    --user-name [USER_NAME]      the user's name, ie that is credited in the LICENSE
    --user-email [USER_EMAIL]    the user's email, ie that is credited in the Gem specification

    --github-username [GITHUB_USERNAME]
                                 name of the user on GitHub to set the project up under
    --github-token [GITHUB_TOKEN]
                                 GitHub token to use for interacting with the GitHub API
    --git-remote [GIT_REMOTE]    URI to set the git origin remote to
    --homepage [HOMEPAGE]        the homepage for your project (defaults to the GitHub repo)
    --no-create-repo             create the repository on GitHub

    --yard                       use yard for documentation
    --rdoc                       use rdoc for documentation
-h, --help                       display this help and exit


Copyright © 2010, 2011 Raoul J.P. Bonnal. See LICENSE.txt for further details.

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