Environment

COBRA is a terminal friendly snake. In order to setup a friendly environment, please be familiar with using terminal. Note that the command below are all based on terminal command.

1.1 Docker

Docker container is a super handly tool which is able to provide a friendly environment for users. Once you have docer installed on you own machine. COBRA provides a Dockerfile to make life easier. What you need to do is just git clone and use the Dockerfile we provided to setup a Docker environment for COBRA.

git clone cobra
cd cobra
docker build -t COBRA:1.0 .

Note that docker build will help you to setup a vitual linux environment with all the software prepared.

1.2 Build your own environment

If you don’t like docker, and you want to see what kind of software COBRA required. Don’t worry, you can setup manually. pip install would be a savior for python dependencies of COBRA once you have COBRA repo downloaded.

pip install -r requirements.txt
python setup.py install

1.3 Other softwares dependencies

In order to enhance COBRA’s abilities, there’re few other softwares required to be installed before you take COBRA home.

a) MEME-Suite

In order to reduce the noise level, we used FIMO in MEME-Suite to do motif filtering for COBRA.

Quick Install for meme-suite

1tar zxf meme_4.11.4.tar.gz
2cd meme_4.11.4
3./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt
4make
5make test
6make install
7
8# configureation
9export PATH=$HOME/meme/bin:$PATH

More details could be found here.

b) Distribution Optimization

This is a R package embedded into COBRA, which provides COBRA a more powerful sense of RNA-seq touch. If you are interested in the package, please click here.