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Files

bmccandless b3e9719602 hosted cellxgene (#38 ) (#1200 )

* early, non-working eb config

* hosted cellxgene

In this PR, contains scripts and instructions for deploying cellxgene
for AWS elastic beanstalk.  It supports the multi-dataset option.

The Makefile in the server/eb directory creates an artifact.zip
file, which can be deploy at AWS EB.

The server/eb directory contains:
  app.py - flask app to run the server
  Makefile - which creates an artifact.zip file which can be deployed.
  README.md - instructions for setting up and deploying the eb app.

* hosted cellxgene (#38)

In this PR, contains scripts and instructions for deploying cellxgene
for AWS elastic beanstalk.  It supports the multi-dataset option.

The Makefile in the server/eb directory creates an artifact.zip
file, which can be deploy at AWS EB.

The server/eb directory contains:
  app.py - flask app to run the server
  Makefile - which creates an artifact.zip file which can be deployed.
  README.md - instructions for setting up and deploying the eb app.

* Update how artifact.zip is created

prune the server/test and server/eb directories

* Remove debugging print statements

* fixes from review comments

* fix lint

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>

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

.ebextensions

hosted cellxgene (#38 ) (#1200 )

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app.py

hosted cellxgene (#38 ) (#1200 )

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

config_deploy.yaml

hosted cellxgene (#38 ) (#1200 )

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

Makefile

hosted cellxgene (#38 ) (#1200 )

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

README.md

hosted cellxgene (#38 ) (#1200 )

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