Iroki

Command line app and library code for Iroki, a phylogenetic tree customization program.

Citation

Iroki is research software. If you use Iroki, please cite the Iroki preprint:

Moore RM, Harrison AO, McAllister SM , Marine RL, Chan CS, and Wommack KE. 2017. Iroki: automatic customization for phylogenetic trees. bioRxiv doi:10.1101/106138

Documentation

For in depth docs and examples, please see the Iroki wiki page.

Installation

Using the web app

Iroki has a web app (iroki.net). The code for that is also on GitHub.

Running with Docker

See the wiki.

Use the command line app with RubyGems

If you already have a working Ruby environment, run this

$ gem install iroki

Then type which iroki and you should see something like this

/Users/mooreryan/.rvm/gems/ruby-2.2.4@iroki/bin/iroki

If so, you are good to go!

To use the library code

Add this line to your application's Gemfile:

gem 'iroki'

And then execute:

$ bundle

Or install it yourself as:

$ gem install iroki

Other programs

Newick format to PhyloXML

• exe/newick_to_phyloxml

This will be installed when you run gem install iroki.

Usage: newick_to_phyloxml tree.newick > tree.phyloxml

Note: No specs for this as of yet.

Development

After checking out the repo, run bin/setup to install dependencies. Then, run rake spec to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.

To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.

Contributing

Bug reports and pull requests are welcome on GitHub at https://github.com/mooreryan/iroki. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.