Iroki

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

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.

Version Info

0.0.1

Migrate from color_tree to Iroki.

0.0.2

Add iroki executable, and use RubyGems for installation.

0.0.3

Add a Dockerfile and a wrapper script for running Iroki with Docker.

0.0.4

Fix the iroki_docker install bug.

0.0.5

Add newick_to_phyloxml script.

0.0.6

Add branch length and bootstraps to newick_to_phyloxml.

0.0.7

Add reorder_nodes script.

0.0.8

  • Add auto coloring with Kelly theme
  • Add ability to color branches and labels separately

0.0.9

  • Add single sample color gradients (one and two color)

0.0.10

  • Fix Jess's bug