Wednesday, March 26, 2014

JointSNVMix Installation on Linux Mint 16 Cython, Pysam Included

JointSNVMix is a software package that consists of a number of tools for calling somatic mutations in tumour/normal paired NGS data.

It requires Python (>= 2.7), Cython (>= 0.13) and Pysam (== 0.5.0).

Python must be installed by default ona Linux machine so I will describe the installation of others and JointSNVMix.

Note this guide may become outdated after some time so please make sure before following all.

Install Cython

You may need Python development headers for these Python packages so make sure you have them:

$ sudo apt-get update
$ sudo apt-get install python-dev
$ sudo apt-get install libevent-dev

To install Cython:

$ cd ~/Downloads
$ wget http://cython.org/release/Cython-0.20.1.tar.gz
$ tar xzvf Cython-0.20.1.tar.gz
$ cd Cython-0.20.1
$ sudo python setup.py install

Install Pysam

Pysam installation requires ez_setup that requires distribute.

To install distribute:

$ cd ~/Downloads
$ wget https://pypi.python.org/packages/source/d/distribute/distribute-0.7.3.zip
$ unzip distribute-0.7.3.zip -d distribute-0.7.3
$ cd distribute-0.7.3
$ sudo python setup.py install

To install ez_setup:

$ cd ~/Downloads
$ wget https://pypi.python.org/packages/source/e/ez_setup/ez_setup-0.9.tar.gz
$ tar xzvf ez_setup-0.9.tar.gz
$ cd ez_setup-0.9
$ sudo python setup.py install 

Ready to install Pysam now:

$ cd ~/Downloads
$ wget http://pysam.googlecode.com/files/pysam-0.5.tar.gz
$ tar xzvf pysam-0.5.tar.gz
$ cd pysam-0.5
$ sudo python setup.py install

Now, install JointSNVMix:

$ cd ~/Downloads
$ wget http://joint-snv-mix.googlecode.com/files/JointSNVMix-0.7.5.tar.gz
$ tar xzvf JointSNVMix-0.7.5.tar.gz
$ cd JointSNVMix-0.7.5
$ sudo python setup.py install

Run

$ jsm.py
usage: JointSNVMix [-h] {train,classify} ...
JointSNVMix: error: too few arguments

Follow running guide for all arguments and options.

No comments: