VM for profiling

This packer configuration creates a VM provisioned with tools need for profiling analysis.

• Python packages
• cytominer-database and dependencies
• Distributed-CellProfiler and dependencies

In addition, it mounts

• an S3 bucket so that CellProfiler can access files
• an NFS (Amazon Elastic File System (EFS))

Install packer

OS X:

brew install packer

Windows:

• Get it here

Building the VM

Authenticate

aws configure

Edit EFS and S3 configurations

Edit EFS_ID in efs.sh, and S3_ROLE and BUCKET_ID is s3.sh appropriately.

Validate and build

Note that although instance specifics are included in cytominer_ami.json (c4.large), and an instance will be created, the instance only exists to create the AMI and will be destroyed upon completion, delete_on_termination: true, leaving only the newly created AMI.

packer validate cytominer_ami.json

Specify security_group_ids, subnet_id and vpc_id on which the builder should be run (get these from AWS console)

packer build  -var 'security_group_ids=sg-NNNNNNNN,sg-NNNNNNNN' -var 'subnet_id=subnet-NNNNNNNN' -var 'vpc_id=vpc-NNNNNNNN' cytominer_ami.json

The security groups should be such that together they allow

• SSH access on port 22
• NFS access on part 2049 (for EFS)