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

We assume your current working directory is the directory into which you've cloned this repository.

0. This project requires python 3.6 or higher. Please check your version with

$ python --version

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. Install the gateway:

To install in development mode:

python setup.py develop

To install from GitHub:

pip install git+https://github.com/Novartis/cellxgene-gateway

To install from PyPI:

# NOT YET DONE, COMING! STAY TUNED

4. 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

5. Set your environment variables correctly:

export CELLXGENE_LOCATION=`which cellxgene`
export CELLXGENE_DATA=../cellxgene_data  # change this directory if you put data in a different place.
export GATEWAY_HOST=localhost:5005
export GATEWAY_PROTOCOL=http
export GATEWAY_IP=127.0.0.1

6. Now, execute the cellxgene gateway:

cellxgene-gateway

For convenience, you can also change run.sh.example and execute it.

Here's what the environment variables mean:

• 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.

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 -l 79 .

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