mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-09-17 13:58:00 +08:00

Files

Bruce Martin d99b84ba09 prepare - work around anndata bug (#1260 )

* work around anndata bug 344

* fix accidental cut and paste error

* Use modified make_index_unique function

Temporarily copy code from https://github.com/theislab/anndata/pull/345
until the issue is resolved and released.

* Add notes and test for make_index_unique

* Lint fix

* Format python

Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>

2020-03-22 12:27:59 -07:00

.ebextensions

fixes for hosted cellxgene (#1227 )

2020-03-16 09:47:01 -07:00

app.py

prepare - work around anndata bug (#1260 )

2020-03-22 12:27:59 -07:00

config_deploy.yaml

hosted cellxgene (#38 ) (#1200 )

2020-03-09 12:08:07 -07:00

Makefile

Introduce a config file to cellxgene (#1264 )

2020-03-22 09:34:11 -07:00

README.md

Introduce a config file to cellxgene (#1264 )

2020-03-22 09:34:11 -07:00

README.md

AWS Elastic Beanstalk

This directory contains script to aid in creating and deploying cellxgene on an AWS Elastic Beanstalk instance.

This will result in a variant of cellxgene, running on AWS EC2 instances, serving data from S3. All datasets must be in the new CXG (tiledb) format - see the converter script cxgtool.py in server/converters - and located in a single S3 prefix, which is accessible to the instance. In the current incarnation, no access control or authentication support is available (outside of anything you configure yourself), so this is most appropriate for public datasets.

This is early development work, and will change significantly in the near future. We would love feedback on it, but please assume it will change.

Prerequisites

Some familiarity with AWS EB, S3, and IAM are needed.
Install the awsebcli. Instruction are here:
https://docs.aws.amazon.com/elasticbeanstalk/latest/dg/eb-cli3-install.html
In the top level directory, run make build-client to create the client static assets.

Steps

These steps are meant to serve as an example.
There are many more options to these commands that may be important or necessary for your environment.

Create an S3 bucket

Upload your matrix files to this bucket
Create an elastic beanstalk application. For example:
```
EB_APP=cellxgene-app
eb init -p python-3.6 $EB_APP
```
Create the artifact.zip file for the application

If you have additional configuration for the application, place that application in server/eb/config.yaml. This will be included in the eb deployment.
```
make build
```

Create an environment

# name of the environment
EB_ENV=cellxgene-env
# type of ec2 instance to run the cellxgene server.     
EB_INSTANCE=m5.large 
CXG_DATAROOT=<location to your S3 bucket>

eb create $EB_ENV --instance-type $EB_INSTANCE --envvars CXG_DATAROOT=$CXG_DATAROOT

Give the elastic beanstalk environment access to the S3 bucket.

This link may provide some useful information: https://aws.amazon.com/premiumsupport/knowledge-center/elastic-beanstalk-s3-bucket-instance/
Deploy the application
```
eb deploy $EB_ENV 
```
Open the application in a browser
```
eb open $EB_ENV
```