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* Introduce a config file to cellxgene The config file format is in yaml. The default config is located in server/common/default_config.py. A user may create a yaml file that contains a subset of these fields. It can be used during cellxgene launch, or for hosted cellxgene. The code has also been refactored. Much of the logic to check arguments has moved from launch to app config. It is now possible to set the tiledb context parameters using the config file. Other feature will soon be handled in a similar way.
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
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/
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Deploy the application
eb deploy $EB_ENV -
Open the application in a browser
eb open $EB_ENV