Iroki

Iroki

Gem Version Build Status Coverage Status GitHub issues GitHub license

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 R, Chan C, Wommack KE. 2017. Iroki: automatic customization for phylogenetic trees. doi: https://doi.org/10.1101/106138

Documentation

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

Installation

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.