Installation and setup

Note

Using the instructions for the IO installation is highly recommended! It may take a little more set-up depending on your operating system, but the benefits during processing are noticeable!

Basic installation

This package requires Python 3.6+. Assuming you have the correct version of Python installed, you can install abagen by opening a terminal and running the following:

pip install abagen

Alternatively, you can install the most up-to-date version of from GitHub:

git clone https://github.com/rmarkello/abagen.git
cd abagen
pip install .

Important

If you are going to install the version directly from GitHub make sure that you are using the most up-to-date documentation!

IO installation

The data supplied by the Allen Human Brain Atlas is quite large—on the order of ~4GB for all six donors. Because loading these datasets into memory can be quite time-consuming, abagen has integrated support for parquet and can do some on-the-fly conversions to speed things up. However, using parquet is completely optional, and therefore support for it is not installed when using the “vanilla” installation procedures.

If you would like to enable parquet support, you will need to install some additional dependencies. This can be done using pip:

pip install abagen[io]

Note

If you are using a Linux OS, you will need to install the libsnappy-dev (Debian) or snappy-devel (Fedora) package before running the above installation command!

You can also install these extra packages from the GitHub source:

git clone https://github.com/rmarkello/abagen.git
cd abagen
pip install .[io]

Important

If you are going to install the version directly from GitHub make sure that you are using the most up-to-date documentation!