Installation

1. Obtain Python 2.7 and virturalenv.

Note

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

2. 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

3. Download the source code and install the requirements.

$ git clone https://github.com/paoyangchen-laboratory/methgo.git
$ pip install -r methgo/requirements/base.txt
$ pip install -r methgo/requirements/addition.txt

Note

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:

• NumPy
• SciPy
• matplotlib
• pandas
• PySAM (0.8.0)
• Biopython
• pyfasta
• Cython
• pybedtools

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