NOTE: THE IROKI COMMAND LINE APP IS NO LONGER MAINTAINED. ALL FUTURE WORK WILL BE WITH THE WEB APP: https://github.com/mooreryan/iroki , www.iroki.net.
Command line app and library code for Iroki, a phylogenetic tree customization program.
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
For in depth docs and examples, please see the Iroki wiki page.
Iroki has a web app (iroki.net). The code for that is also on GitHub.
See the wiki.
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!
Add this line to your application's Gemfile:
gem 'iroki'And then execute:
$ bundle
Or install it yourself as:
$ gem install iroki
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.
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.
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.