= Biogem

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
http://rubygems.org. Biogems are automatically listed at
http://biogems.info

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 github.com and/or rubygems.org and
packaging. Bundler is used used for setting up a predefined developing
environment.

Also Biogem makes use of webservices. E.g.

* GitHub.com and RubyGems.org
  are two different services and you need to create different accounts for them
  if you already use GitHub.com you are set for using Biogem

== Biogems Official Archive

* http://biogems.info/ 

== Biogem Tutorial

The latest version is on https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc 

== Contributing to Biogem

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

=== StepByStep

Toshiaki Katayama wrote a step by step guide for a bio-foobar plugin @ http://bioruby.open-bio.org/wiki/BiogemInstallation.

== BioRuby's Wiki Official Documentation

* http://bioruby.open-bio.org/wiki/Plugins
* http://biogems.info/ official collector for BioRuby plugins

== 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

Copyright (c) 2010, 2011 Raoul J.P. Bonnal. See LICENSE.txt for
further details.