bio-sambamba

Full description goes here

Note: this software is under active development!

Installation

    rake build
    rake install

In order to use the gem, you also need sambamba tool installed (version >= 0.2.6).

If you use Debian, you can download a package for your architecture from github downloads.

Otherwise, you need to do the following:

• install DMD compiler

• install Ragel finite state machine compiler

• On Mac OS X you can install homebrew package manager, then install dmd and ragel easily with

    brew install dmd
    brew install ragel

• On Arch Linux you can use pacman to install dmd and ragel

    pacman -S dmd libphobos ragel

• clone sambamba repository and compile the tool

    git clone https://github.com/lomereiter/sambamba.git
    cd sambamba/CLItools/
    make

• place the executable file build/sambamba to somewhere in your $PATH, for example:

    cp build/sambamba /usr/local/bin

Usage

    require 'bio-sambamba'

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/lomereiter/bioruby-sambamba

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
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Biogems.info

This Biogem is published at #bio-sambamba

Copyright

Copyright (c) 2012 Artem Tarasov. See LICENSE.txt for further details.