You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
georgeG ea02ba844a formatting 5 years ago
bin Merge branch 'live' 5 years ago
doc formatting 5 years ago
etc Adds 8 gems from mjy/Species File Group. With the exception of sqed all others have been used to do useful work, several in production. 6 years ago
features Added Rubygems API test 6 years ago
lib Merge branch 'live' 5 years ago
scripts Merge pull request #74 from pjotrp/live 6 years ago
source Meta tags 6 years ago
test/data Rename YAML 6 years ago
.gitignore Rakefile: script name 6 years ago
Gemfile Tokens and geminfo 6 years ago
Gemfile.lock Tokens and geminfo 6 years ago Rewrite website from staticmatic to middleman 6 years ago
README.rdoc Updated year 6 years ago
Rakefile Rakefile: script name 6 years ago
config.rb Rewrite website from staticmatic to middleman 6 years ago



The following information describes the steps to getting your biogem
registered on If you are looking to generate the website instead: read! tracks interesting Ruby gems for bioinformatics.

To get your gem listed, simply create a gem named 'bio-mygem', i.e.
start the name with bio dash, and push it onto You can
use the biogem tool to create the plumbing, if you like. If you wish
to name your gem differently, or host the gem elsewhere, it can still
be listed. Either add a project description to /etc/biogems/name.yaml,
or add an issue to the github tracker at

= Gem settings

The settings displayed, on, are the ones you specify
for a gem. In particular = "bio-gem"
gem.homepage = ""
gem.license = "MIT"
gem.summary = %Q{BioGem helps Bioinformaticians start developing plugins/modules for BioRuby creating a scaffold and a gem package}
gem.description = %Q{BioGem is a scaffold generator for those
... } = ""
gem.authors = ["Raoul J.P. Bonnal"]

This is the information pushed to when releasing a
gem. harvests this information, with the download statistics.

= Additional settings

Information, not available through gems, is captured through overriding
settings. These are stored in this source repository, under ./etc/biogems/.
These files add information, such as doi references, and the status of a gem
(core, stable, test), but also potentially override gem settings, such
as the summary field(!)

For example in ./etc/biogems/bio.yaml

# Additional BioRuby settings
:doi: 10.1093/bioinformatics/btq475
:status: core

It is also possible the overriding gemname.yaml is in your github
repository(!) Just tell us where it resides through

= GitHub API access limits

Without using authentication, the GitHub API allows only 60 requests
per hour from a single IP address. But during the data collection
phase of generating the website, the script currently
needs to make around 200 requests to this API to fetch the number of
issues and stargazers for each gem.

To get around this, go to the applications tab on your GitHub
settings page and generate a new "Personal API access token". Then
copy that token (but not into the repository!), and before running the ./ script,
set the GITHUB_API_TOKEN environment variable like this:

export GITHUB_API_TOKEN="copy-here-the-token-string-from-github"

That lets the script make 5000 requests per hour, which should be
more then enough.

= Website source

This repository on github contains the source code for the website. is an initiative by the BioRuby developers
Copyright (C) 2011,2012,2013,2014 Pjotr Prins <>