Set up more or less standard biogem skeleton.

.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

.gitignore

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+# rcov generated
+coverage
+coverage.data
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
+#
+# For MacOS:
+#
+#.DS_Store
+
+# For TextMate
+#*.tmproj
+#tmtags
+
+# For emacs:
+#*~
+#\#*
+#.\#*
+
+# For vim:
+#*.swp
+
+# For redcar:
+#.redcar
+
+# For rubinius:
+#*.rbc
+# Ignore Gemfile.lock for gems. See http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/
+Gemfile.lock
+*.gemspec

.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+#  - jruby-19mode # JRuby in 1.9 mode
+#  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+gem "bio", "~> 1.4.2"
+gem "libxml-ruby", "~> 2.3.2"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.1.0"
+  gem "jeweler", "~> 1.8.3"
+end

LICENSE.txt

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+Copyright (c) 2012 Clayton Wheeler
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

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+# bio-phyloxml
+
+[![Build Status](https://secure.travis-ci.org/csw/bioruby-phyloxml.png)](http://travis-ci.org/csw/bioruby-phyloxml)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-phyloxml
+```
+
+## Usage
+
+```ruby
+    require 'bio-phyloxml'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/csw/bioruby-phyloxml
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-phyloxml](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2012 Clayton Wheeler. See LICENSE.txt for further details.
+

README.rdoc

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+= bio-phyloxml
+
+{<img
+src="https://secure.travis-ci.org/csw/bioruby-phyloxml.png"
+/>}[http://travis-ci.org/#!/csw/bioruby-phyloxml]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-phyloxml
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-phyloxml'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/csw/bioruby-phyloxml
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-phyloxml
+
+== Copyright
+
+Copyright (c) 2012 Clayton Wheeler. See LICENSE.txt for further details.
+

Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-phyloxml"
+  gem.homepage = "http://github.com/csw/bioruby-phyloxml"
+  gem.license = "MIT"
+  gem.summary = %Q{PhyloXML plugin for BioRuby}
+  gem.description = %Q{Provides PhyloXML support for BioRuby.}
+  gem.email = "cswh@umich.edu"
+  gem.authors = ["Diana Jaunzeikare", "Clayton Wheeler"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-phyloxml #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

VERSION

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+1.0.0

test/helper.rb

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+require 'pathname'
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+
+unless defined? BioRubyTestDataPath and BioRubyTestDataPath
+  test_data_path = Pathname.new(File.join(File.dirname(__FILE__),
+                                          "data")).cleanpath.to_s
+  test_data_path.freeze
+  BioRubyTestDataPath = test_data_path
+end
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-phyloxml'
+
+class Test::Unit::TestCase
+end