1. Obtain Python 2.7 and virturalenv.


MethGo depends on SAMtools and BEDtools, so please make sure you already have them on your server.

  1. Create a virtual environment somewhere on your disk, and then activate it.
$ virtualenv --no-site-packages --python=python2.7 methgo_env
$ source methgo_env/bin/activate
  1. Download the source code and install the requirements.
$ git clone
$ pip install -r methgo/requirements/base.txt
$ pip install -r methgo/requirements/addition.txt


If you’re using Mac and the OS version is larger than 10.8, run the following line before you install the requirements:

$ export CFLAGS=-Qunused-arguments

pip will install the following packages:

  1. Add your MethGo path to the PATH environment variable.