/bioscala

Scala code for bioinformatics

Primary LanguageScala

BioScala

A bioinformatics library made with the Scala Language.

This project is in it's early days with a minimum function to read fasta files and principaly some code to deal with the Velvet Graph File.

Prerequisites

  1. Maven >= 2 http://maven.apache.org/

  2. Scala Language >= 2.8 http://www.scala-lang.org/

How to Download the Source

Use the git SCM software with the command:

git clone git://github.com/lvaruzza/bioscala.git

Git is available in most of the Linux distributions and in the site:

http://git-scm.com/

How to compile

mvn install

How to run the commands

The commands are availiable as shell scripts in bin directory

Example:

./bin/dumpContigs velvet preprocessor/colorspace_input.csfasta contigs