Overview

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets. It displays an index of available h5ad (anndata) files. When a user clicks on a file name, it launches a Cellxgene Server instance that loads that particular data file and once it is available proxies requests to that server.

Running locally

1. Set up a venv with

   python -m venv .cellxgene-gateway source .cellxgene-gateway/bin/activate

2. Install requirements with

   pip install -r requirements.txt

3. Prepare a folder with .h5ad files, for example

   mkdir cellxgene_data wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad

4. Copy run.sh.example to run.sh and edit if you want to change venv or .h5ad folder position:

cp run.sh.example run.sh

run.sh defines various environment variables:

• DEPLOYMENT_ENV - expects 'dev', 'tst' or 'prd'
• CELLXGENE_LOCATION - the location of the cellxgene executable, e.g. ~/anaconda2/envs/cellxgene/bin/cellxgene
• CELLXGENE_DATA - a directory that can contain subdirectories with .h5ad data files, without trailing slash, e.g. /mnt/cellxgene_data
• GATEWAY_HOST - the hostname and port that the gateway will run on, typically localhost:5005 if running locally
• GATEWAY_PROTOCOL - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.

The defaults should be fine if you set up a venv and cellxgene_data folder as above.

5. Finally, execute run.sh:

source run.sh

Customization

The current paradigm for customization is to modify files during a build or deployment phase:

• To modify CSS or JS on particular gateway pages, overwrite or append to the templates
• To add script tags such as for user analytics to all pages, overwrite the extra_scripts.py file.
  • these scripts will also be run on the pages served by cellxgene server via the --scripts parameter
  • See https://github.com/chanzuckerberg/cellxgene/pull/680 for details on --scripts parameter

Currently we use a build.sh that copies the gateway to a "build" directory before modifying with sed and the like.

Development

Running Linters

pip install isort flake8 black

isort -rc .

flake8 .

black .

Getting Help

If you need help for any reason, please make a github ticket. One of the contributors should help you out.

Contributors

• Niket Patel - https://github.com/NiketPatel9
• Alok Saldanha - https://github.com/alokito
• Yohann Potier - https://github.com/ypotier