Plugins

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

Pre-requisites

 * Ruby: Ruby: 1.9
 * development and installation have been tested on 1.9.2, 1.9.3.


 * RVM: RVM http://beginrescueend.com/ is optional, but suggested. Not only can you specify the Ruby interpreter version that works best with Biogem, RVM also allows multiple ruby interpreters in your home directory for testing purposes. When using RVM, make sure to compile with openssl support, e.g. on Debian

$ sudo apt-get install libssl-dev $ rvm install 1.9.3 --with-openssl-dir=$HOME/.rvm/usr


 * GitHub &amp; RubyGems: In order to use Biogem to its fullest potential, you must create a regular GitHub http://github.com and  RubyGems http://rubygems.org account. Why? Because for sharing and keeping track of source code we (currenlty) use github and for distributing the plugin we rely on RubyGems, the reference Ruby gem repository. To configure github and automate most of Biogem's tasks:

$ git config --global user.name "Firstname Lastname" Sets the name of the user for all git instances on the system $ git config --global user.email "your_email@youremail.com" $ git config --global github.user "user_id" $ git config --global github.token "TOKEN ASSIGNED BY GITHUB"

Note: another Ruby version management system used in BioRuby community is https://github.com/sstephenson/rbenv but for now we can not provide support for it.

IMPORTANT NOTE
Rubygems will not let you install Biogem in an environment with a Ruby interpreter older than 1.9

Download
Install the Biogem toolset with

$ gem install bio-gem

all the required dependencies will be downloaded and installed automatically.

$ gem install bio-gem Fetching: rake-0.9.2.2.gem (100%) Fetching: git-1.2.5.gem (100%) Fetching: jeweler-1.6.4.gem (100%) Fetching: json-1.6.4.gem (100%) Building native extensions. This could take a while... Fetching: rdoc-3.12.gem (100%) Depending on your version of ruby, you may need to install ruby rdoc/ri data: &lt;= 1.8.6 : unsupported = 1.8.7 : gem install rdoc-data; rdoc-data --install = 1.9.1 : gem install rdoc-data; rdoc-data --install &gt;= 1.9.2 : nothing to do! Yay! Fetching: bio-gem-1.2.0.gem (100%) Successfully installed rake-0.9.2.2 Successfully installed git-1.2.5 Successfully installed jeweler-1.6.4 Successfully installed json-1.6.4 Successfully installed rdoc-3.12 Successfully installed bio-gem-1.2.0 6 gems installed Installing ri documentation for rake-0.9.2.2... Installing ri documentation for git-1.2.5... Installing ri documentation for jeweler-1.6.4... Installing ri documentation for json-1.6.4... Installing ri documentation for rdoc-3.12... Installing ri documentation for bio-gem-1.2.0... Installing RDoc documentation for rake-0.9.2.2... Installing RDoc documentation for git-1.2.5... Installing RDoc documentation for jeweler-1.6.4... Installing RDoc documentation for json-1.6.4... Installing RDoc documentation for rdoc-3.12... Installing RDoc documentation for bio-gem-1.2.0...

Note: the above list of dependencies is just an example and it may vary from your current installation.

Browse the documentation
During the installation you may note how Rubygems install the documentation for you, for each library installed. Is possible to access to all the documentations and API installed simply typing in the command line:

$ gem server Server started at http://0.0.0.0:8808 Server started at http://[::ffff:0.0.0.0]:8808

To see Biogem documentation locally use this link:

http://localhost:8808/doc_root/bio-gem-1.2.0/rdoc/README_rdoc.html

Note: the above link must be update with your current version of Biogem

Biogem Tutorial HowTo Develop a plugins
Please follow the guide reported in tutorial https://github.com/helios/bioruby-gem/blob/master/Tutorial.rdoc, which is the most up to date version. You'll find out how to create:


 * a simple plugin
 * embed a database
 * create a Biogem Engine to embed your gem into a Ruby on Rails web application

and much more

Biogems Official Archive

 * http://biogems.info

Contributing to Biogem
The source code repositories for Biogem and http://biogems.info website are on github.


 * https://github.com/helios/bioruby-gem
 * https://github.com/pjotrp/biogems.info

If you want to contribute, feel free! Clone the project!

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

Note: this page is generated using the README.rdoc from the development repository listed above, and has been adapted to fit into the this Wiki. The documentation generated in the early days of Biogem is still available Plugins-OriginalStory but is DEPRECATED.