Topics

#dataviz #h5ad #rna-seq #scientific #scrna-seq #transcriptomics #visualization

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README

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

Prequisites

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

$ python --version

It is also a good idea to set up a venv

python -m venv .cellxgene-gateway
source .cellxgene-gateway/bin/activate # type deactivate to deactivate the venv

Install cellxgene-gateway

Option 1: Pip Install from Github

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

Note: you may need to downgrade h5py with pip install h5py==2.9.0 due to an issue in a dependency.

Option 2: Install from PyPI

pip install cellxgene-gateway

Running cellxgene gateway

Prepare a folder with .h5ad files, for example

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

Set your environment variables correctly:

export CELLXGENEDATA=../cellxgenedata  # change this directory if you put data in a different place.
export CELLXGENE_LOCATION=which cellxgene

Now, execute the cellxgene gateway:

cellxgene-gateway

Here's what the environment variables mean:

CELLXGENE_LOCATION - the location of the cellxgene executable, e.g. ~/anaconda2/envs/cellxgene/bin/cellxgene

At least one of the following is required: CELLXGENEDATA - a directory that can contain subdirectories with .h5ad data files, without* trailing slash, e.g. /mnt/cellxgenedata

CELLXGENE_BUCKET - an s3 bucket that can contain keys with .h5ad data files, e.g. my-cellxgene-data-bucket

Cellxgene Gateway is designed to make it easy to add additional data sources, please see the source code for gateway.py and the ItemSource interface in items/item_source.py

Optional environment variables:

CELLXGENE_ARGS - catch-all variable that can be used to pass additional command line args to cellxgene server
EXTERNALHOST - the hostname and port from the perspective of the web browser, typically localhost:5005 if running locally. Defaults to "localhost:{GATEWAYPORT}"
EXTERNAL_PROTOCOL - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy that performs https termination. Default value "http"
GATEWAY_IP - ip addess of instance gateway is running on, mostly used to display SSH instructions. Defaults to socket.gethostbyname(socket.gethostname())
GATEWAY_PORT - local port that the gateway should bind to, defaults to 5005
GATEWAYEXPIRESECONDS - time in seconds that a cellxgene process will remain idle before being terminated. Defaults to 3600 (one hour)
GATEWAYEXTRASCRIPTS - JSON array of script paths, will be embedded into each page and forwarded with --scripts to cellxgene server
GATEWAYENABLEANNOTATIONS - Set to true or to 1 to enable cellxgene annotations and gene sets.
GATEWAYENABLEBACKED_MODE - Set to true or to 1 to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.
GATEWAYLOGLEVEL - default is INFO. set to DEBUG to increase logging and to WARNING to decrease logging.
S3ENABLELISTINGS_CACHE - Set to true or to 1 to cache listings of S3 folders for performance. If the cache becomes stale, set filecrawl.html?refresh=true query parameter to refresh the cache.

If any of the following optional variables are set, ProxyFix will be used.

PROXYFIXFOR - Number of upstream proxies setting X-Forwarded-For
PROXYFIXPROTO - Number of upstream proxies setting X-Forwarded-Proto
PROXYFIXHOST - Number of upstream proxies setting X-Forwarded-Host
PROXYFIXPORT - Number of upstream proxies setting X-Forwarded-Port
PROXYFIXPREFIX - Number of upstream proxies setting X-Forwarded-Prefix

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

Running cellxgene-gateway with Docker

First, build Docker image:

docker build -t cellxgene-gateway .

Then, cellxgene-gateway can be launched as such:

docker run -it --rm \
-v <localdatadir>:/cellxgene-data \
-p 5005:5005 \
cellxgene-gateway

Additional environment variables can be provided with the -e parameter:

docker run -it --rm \
-v ../cellxgene_data:/cellxgene-data \
-e GATEWAY_PORT=8080 \
-p 8080:8080 \
cellxgene-gateway

Running cellxgene gateway with start scripts

For your convenience, we provide start scripts for flask, gunicorn and uwsgi.

First, set up a .env

cp env_example .env edit .env
 open .env

Then run the scripts in a subshell

( ./start_flask.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, set GATEWAYEXTRASCRIPTS

* 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 bash script that copies the gateway to a "build" directory before modifying templates with sed and the like. There is probably a better way.

Development

We’re actively developing. Please see the "future work" section of the wiki. If you’re interested in being a contributor please reach out to @alokito.

Developer Install

If you want to develop the code, you will need to clone the repo. Make sure you have the prequesite listed above, then:

Clone the repo

git clone https://github.com/Novartis/cellxgene-gateway.git
    cd cellxgene-gateway

Install requirements with

pip install -r requirements.txt

Install the gateway in developer mode

python setup.py develop

For convenience, the code repo includes a run.sh.example shell script to run the gateway.

Install pre-commit hooks

conda install -c conda-forge pre-commit
pre-commit install

Running Tests

python -m unittest discover tests

Code Coverage

coverage run -m unittest discover tests
    coverage html

Running Linters

pip install isort flake8 black

isort -rc . # rc means recursive, and was deprecated in dev version of isort
black .

Getting Help

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

Releasing New Versions

How to prepare for release

Update Changelog.md and version number in init.py
Cut a release on github

- Go to your project homepage on GitHub - On right side, you will see Releases link. Click on it. - Click on Draft a new release - Fill in all the details - Tag version should be the version number of your package release - Release Title can be anything you want, but we use v0.3.11 (the same as the tag to be created on publish) - Description should be changelog - Click Publish release at the bottom of the page - Now under Releases you can view all of your releases. - Copy the download link (tar.gz) and save it somewhere

How to publish to PyPI

Make sure your .pypirc is set up for testpypi and pypi index servers.

rm -rf dist
python setup.py sdist bdist_wheel
python -m twine upload --repository testpypi dist/*
python -m twine upload dist/*

Contributors

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

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