Quick installation using pip

The following assumes you have pip on your system (this comes standard with new Macs for instance), that you have made a virtualenv or a conda environment and that you’re connected to the internet.

The key steps for the minimal install are:

  1. Install numpy

    $ pip install numpy
    
  2. Use pip to download, build and install PyCogent.

    $ pip install cogent
    

If the above fails to download PyCogent you can download an archive to your hard drive and then do.

$ pip install path/to/pycogent-master.zip

Optional installs

To use the Ensembl querying code

$ pip install cogent[mysql]

To use the parallel capabilities

$ pip install cogent[mpi]

To install all dependencies

$ pip install cogent[all]

This will install all the above and matplotlib for drawing

To use the development version of PyCogent

Just replace the first line of the requirements file with git+https://github.com/pycogent/pycogent.git.