8a733270d7
* Fix for favicon with --dataroot * fix static assets in hosted cxg The web proxy at aws eb was not finding the static assets. The solution here is very simple: just copy the directory containing the static assets to the top level of the artifact.zip. This is not really the ideal solution. According to the AWS docs you can make a mapping to the correct location in an an ebextentions config file. I tried this and many combinations but was not able to get this to work following that pattern. Since we control the construction of the zip file, the solution here isn't bad, but it could probably be made better.
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
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Some familiarity with AWS EB, S3, and IAM are needed.
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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-clientto 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.
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Create an S3 bucket
Upload your matrix files to this bucket
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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/
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Deploy the application
eb deploy $EB_ENV -
Open the application in a browser
eb open $EB_ENV