BioHPC

...

Database

Where is the DB hosted

Our BioHPC database is hosted on cbsujohnson.biohpc.cornell.edu. Once you created a BioHPC account, you can ssh to the machine using

...

This container is created and run by Zack, one of our previous team members, and the script he used is located at /workdir/ztb5/mongo/.

How to backup/restore the DB

Currently, the backup is done by a Cron job that executes the script /home/ts864/mongoDbBackup/dumpJob.sh at 4:00 AM every day. The content of the script is provided below

...

mongorestore --uri=<target DB URI> --drop path-to-backup-folder/

AWS

Lambda

When creating an AWS Lambda, make sure to use cu-cals-johnson-lab-vpc for VPC and choose both cu-cals-johnson-lab-subnet-private-1 and cu-cals-johnson-lab-subnet-private-2 for subnets. This can be done during the creation of a new Lambda or in the Configuration tab of an existing Lambda.

EC2

The EC2 instances used for deploying backend services are created following the procedure starting from step 3 of this tutorial (https://medium.com/@umairnadeem/deploy-to-aws-using-docker-compose-simple-210d71f43e67) with the following modifications.

1. When creating an instance, we reuse existing key pairs instead of creating new ones.
2. We retrieve our codebase using git instead of scp.