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PyCogent 1.9 documentation

# 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`.