JointSNVMix Installation on Linux Mint 16 Cython, Pysam Included
By Güngör Budak
- 2 minutes read - 238 wordsJointSNVMix 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Note this guide may become outdated after some time so please make sure before following all.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:
1$ sudo apt-get update
2$ sudo apt-get install python-dev
3$ sudo apt-get install libevent-dev
To install Cython:
1$ cd ~/Downloads
2$ wget http://cython.org/release/Cython-0.20.1.tar.gz
3$ tar xzvf Cython-0.20.1.tar.gz
4$ cd Cython-0.20.1
5$ sudo python setup.py install
Install Pysam
Pysam installation requires ez_setup that requires distribute.
To install distribute:
1$ cd ~/Downloads
2$ wget https://pypi.python.org/packages/source/d/distribute/distribute-0.7.3.zip
3$ unzip distribute-0.7.3.zip -d distribute-0.7.3
4$ cd distribute-0.7.3
5$ sudo python setup.py install
To install ez_setup:
1$ cd ~/Downloads
2$ wget https://pypi.python.org/packages/source/e/ez_setup/ez_setup-0.9.tar.gz
3$ tar xzvf ez_setup-0.9.tar.gz
4$ cd ez_setup-0.9
5$ sudo python setup.py install
Ready to install Pysam now:
1$ cd ~/Downloads
2$ wget http://pysam.googlecode.com/files/pysam-0.5.tar.gz
3$ tar xzvf pysam-0.5.tar.gz
4$ cd pysam-0.5
5$ sudo python setup.py install
Now, install JointSNVMix:
1$ cd ~/Downloads
2$ wget http://joint-snv-mix.googlecode.com/files/JointSNVMix-0.7.5.tar.gz
3$ tar xzvf JointSNVMix-0.7.5.tar.gz
4$ cd JointSNVMix-0.7.5
5$ sudo python setup.py install
Run
1$ jsm.py
2usage: JointSNVMix [-h] {train,classify} ...
3JointSNVMix: error: too few arguments
Follow running guide for all arguments and options.