bio-samtools

Rake is a Make-like program implemented in Ruby. Tasks and dependencies are specified in standard Ruby syntax. Rake has the following features: * Rakefiles (rake's version of Makefiles) are completely defined in standard Ruby syntax. No XML files to edit. No quirky Makefile syntax to worry about (is that a tab or a space?) * Users can specify tasks with prerequisites. * Rake supports rule patterns to synthesize implicit tasks. * Flexible FileLists that act like arrays but know about manipulating file names and paths. * Supports parallel execution of tasks.

An IRB alternative and runtime developer console.

BDD for Ruby.

Ruby on Rails is a full-stack web framework optimized for programmer happiness and sustainable productivity. It encourages beautiful code by favoring convention over configuration.

Code coverage for Ruby 1.9+ with a powerful configuration library and automatic merging of coverage across test suites.

Puma is a simple, fast, threaded, and highly concurrent HTTP 1.1 server for Ruby/Rack applications. Puma is intended for use in both development and production environments. It's great for highly concurrent Ruby implementations such as Rubinius and JRuby as well as as providing process worker support to support CRuby well.

Pg is the Ruby interface to the {PostgreSQL RDBMS}[http://www.postgresql.org/]. It works with {PostgreSQL 9.2 and later}[http://www.postgresql.org/support/versioning/]. A small example usage: #!/usr/bin/env ruby require 'pg' # Output a table of current connections to the DB conn = PG.connect( dbname: 'sales' ) conn.exec( "SELECT * FROM pg_stat_activity" ) do |result| puts " PID | User | Query" result.each do |row| puts " %7d | %-16s | %s " % row.values_at('procpid', 'usename', 'current_query') end end.

Rspec-rails is a testing framework for Rails 3+.

Automatic Ruby code style checking tool. Aims to enforce the community-driven Ruby Style Guide.

Byebug is a Ruby debugger. It's implemented using the TracePoint C API for execution control and the Debug Inspector C API for call stack navigation. The core component provides support that front-ends can build on. It provides breakpoint handling and bindings for stack frames among other things and it comes with an easy to use command line interface.

Uglifier minifies JavaScript files by wrapping UglifyJS to be accessible in Ruby.

TZInfo::Data contains data from the IANA Time Zone database packaged as Ruby modules for use with TZInfo.

Capybara is an integration testing tool for rack based web applications. It simulates how a user would interact with a website.

WebMock allows stubbing HTTP requests and setting expectations on HTTP requests.

Sass adapter for the Rails asset pipeline.

Nokogiri (鋸) is an HTML, XML, SAX, and Reader parser. Among Nokogiri's many features is the ability to search documents via XPath or CSS3 selectors.

This is a JSON implementation as a Ruby extension in C.

Thor is a toolkit for building powerful command-line interfaces.

Jekyll is a simple, blog aware, static site generator.

A toolkit of support libraries and Ruby core extensions extracted from the Rails framework. Rich support for multibyte strings, internationalization, time zones, and testing.

This module allows Ruby programs to interface with the SQLite3 database engine (http://www.sqlite.org). You must have the SQLite engine installed in order to build this module. Note that this module is only compatible with SQLite 3.6.16 or newer.

Minitest provides a complete suite of testing facilities supporting TDD, BDD, mocking, and benchmarking. "I had a class with Jim Weirich on testing last week and we were allowed to choose our testing frameworks. Kirk Haines and I were paired up and we cracked open the code for a few test frameworks... I MUST say that minitest is *very* readable / understandable compared to the 'other two' options we looked at. Nicely done and thank you for helping us keep our mental sanity." -- Wayne E. Seguin minitest/test is a small and incredibly fast unit testing framework. It provides a rich set of assertions to make your tests clean and readable. minitest/spec is a functionally complete spec engine. It hooks onto minitest/test and seamlessly bridges test assertions over to spec expectations. minitest/benchmark is an awesome way to assert the performance of your algorithms in a repeatable manner. Now you can assert that your newb co-worker doesn't replace your linear algorithm with an exponential one! minitest/mock by Steven Baker, is a beautifully tiny mock (and stub) object framework. minitest/pride shows pride in testing and adds coloring to your test output. I guess it is an example of how to write IO pipes too. :P minitest/test is meant to have a clean implementation for language implementors that need a minimal set of methods to bootstrap a working test suite. For example, there is no magic involved for test-case discovery. "Again, I can't praise enough the idea of a testing/specing framework that I can actually read in full in one sitting!" -- Piotr Szotkowski Comparing to rspec: rspec is a testing DSL. minitest is ruby. -- Adam Hawkins, "Bow Before MiniTest" minitest doesn't reinvent anything that ruby already provides, like: classes, modules, inheritance, methods. This means you only have to learn ruby to use minitest and all of your regular OO practices like extract-method refactorings still apply.

Preloads your application so things like console, rake and tests run faster.

The Listen gem listens to file modifications and notifies you about the changes. Works everywhere!.

This gem provides jQuery and the jQuery-ujs driver for your Rails 4+ application.

Makes http fun! Also, makes consuming restful web services dead easy.

AWS Ruby Library for interfacing with Amazon Web Services including EC2, S3, SQS, SimpleDB and most of their other services as well. By http://www.appoxy.com.

Create JSON structures via a Builder-style DSL.

Ruby/Git is a Ruby library that can be used to create, read and manipulate Git repositories by wrapping system calls to the git binary.

Sinatra is a DSL for quickly creating web applications in Ruby with minimal effort.

YARD is a documentation generation tool for the Ruby programming language. It enables the user to generate consistent, usable documentation that can be exported to a number of formats very easily, and also supports extending for custom Ruby constructs such as custom class level definitions.

Faker, a port of Data::Faker from Perl, is used to easily generate fake data: names, addresses, phone numbers, etc.

WebDriver is a tool for writing automated tests of websites. It aims to mimic the behaviour of a real user, and as such interacts with the HTML of the application.

CoffeeScript adapter for the Rails asset pipeline.

Capistrano is a utility and framework for executing commands in parallel on multiple remote machines, via SSH.

Databases on Rails. Build a persistent domain model by mapping database tables to Ruby classes. Strong conventions for associations, validations, aggregations, migrations, and testing come baked-in.

A debugging tool for your Ruby on Rails applications.

A simple HTTP and REST client for Ruby, inspired by the Sinatra microframework style of specifying actions: get, put, post, delete.

Rack provides a minimal, modular and adaptable interface for developing web applications in Ruby. By wrapping HTTP requests and responses in the simplest way possible, it unifies and distills the API for web servers, web frameworks, and software in between (the so-called middleware) into a single method call. Also see https://rack.github.io/.

A gem providing "time travel" and "time freezing" capabilities, making it dead simple to test time-dependent code. It provides a unified method to mock Time.now, Date.today, and DateTime.now in a single call.

Guard::RSpec automatically run your specs (much like autotest).

A fast, safe and extensible Markdown to (X)HTML parser.

HTTP/REST API client library.

Combine 'pry' with 'byebug'. Adds 'step', 'next', 'finish', 'continue' and 'break' commands to control execution.

CocoaPods manages library dependencies for your Xcode project. You specify the dependencies for your project in one easy text file. CocoaPods resolves dependencies between libraries, fetches source code for the dependencies, and creates and maintains an Xcode workspace to build your project. Ultimately, the goal is to improve discoverability of, and engagement in, third party open-source libraries, by creating a more centralized ecosystem.

Rubygem for providing Mozilla's CA Bundle.

Strategies for cleaning databases. Can be used to ensure a clean state for testing.

A simple, fast Mysql library for Ruby, binding to libmysql.

Behaviour Driven Development with elegance and joy.

Rails engine for Turbolinks 5 support.