Installation

Dependencies

You must be on a Linux or MacOS system, with the following installed:

• Python 3.7 to 3.10 (3.11 is not yet supported)

• Jupyter or some other means of running notebooks (e.g., vscode)

For now, it is recommended that you do all this on a host with sufficient memory, and a high bandwidth connection to AWS S3 in the us-west-2 region, e.g., an m6i.8xlarge. If you utilize AWS, Ubuntu 20 or 22 AMI are recommended (AWS AMI should work fine, but has not been tested).

I also recommend you use a d instance type, and mount all of the NVME drives as swap, as it will keep you from running out of RAM.

Set up Python environment

1. (optional, but highly recommended) In your working directory, make and activate a virtual environment. For example:

$ python -m venv ./venv
$ source ./venv/bin/activate

2. Install the cellxgene_census package using pip:

$ pip install -U cellxgene-census

3. Install other third-party packages needed to run the notebooks:

$ pip install scikit-misc scvi-tools

Verify your installation

Check that your installation works - this make take a few seconds, as it loads metadata from S3:

$ python -c 'import cellxgene_census; print(cellxgene_census.open_soma().soma_type)'
SOMACollection

Latest development version

If you want to work with the latest development version of cellxgene-census, you can simply clone the repository and, from the root directory, install locally via pip:

$ git clone https://github.com/chanzuckerberg/cellxgene-census.git
$ cd cellxgene-census
$ pip install -e api/python/cellxgene_census/