lomereiter/bioruby-sambamba

# bio-sambamba

[![Code Climate](https://codeclimate.com/badge.png)](https://codeclimate.com/github/lomereiter/bioruby-sambamba)
[![Build Status](https://secure.travis-ci.org/lomereiter/bioruby-sambamba.png)](http://travis-ci.org/lomereiter/bioruby-sambamba)

Full description goes here

Note: this software is under active development!

## Installation

```sh
    rake build
    rake install
```

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

If you use Debian, you can download a package for your architecture from
[github downloads](http://github.com/lomereiter/sambamba/downloads).

Otherwise, you need to install [DMD compiler](http://dlang.org/download.html).

* On Mac OS X you can install [homebrew](http://mxcl.github.com/homebrew/) package manager, 
then install dmd easily with 

```sh
    brew install dmd
```

* On Arch Linux you can use pacman to install dmd

```sh
    pacman -S dmd libphobos
```

* clone sambamba repository and compile the tool

```sh
    git clone --recursive https://github.com/lomereiter/sambamba.git
    cd sambamba/
    make
```

* place the executable file <code>build/sambamba</code> to somewhere in your $PATH,
  for example:

```sh
    cp build/sambamba /usr/local/bin
```

## Usage

```ruby
    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](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-sambamba](http://biogems.info/index.html)

## Copyright

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