Farmers report

Usage

To use within Sanger just load SoftPack environment and start RStudio

module load HGI/softpack/groups/hgi/farmers-report
module load HGI/common/rstudio
rstudio start -M 8000

You can now knit report or serve an app.

Development

To run tests simply execute within an environment

Rscript tests/testthat.R

To calculate the coverage

Rscript tests/covr.R

The coverage reports can be found in reports/ directory.

To build a Docker image

docker build -t mercury/farmers-report:latest .

To run tests inside a container

docker run --rm -v $(pwd):/code -w /code mercury/farmers-report:latest Rscript /code/tests/testthat.R

Deployment

Infrastructure

Infrastructure is managed via Terraform with a remote backend in a s3 bucket to enable shared access to Terraform state file. Code contains instructions to create an OpenStack VM and configure it as follows.

Terraform creates all cloud resources and do not reuse any existing objects. It creates

• keypair
• network and subnetwork
• external floating IP
• security group with open 8080 port
• VM
• DNS record

OpenStack instance is configured using cloud-config defined in terraform/startup.yaml. It

• mounts NFS (nfs.mount systemd service)
• writes config files (for SMB mount, go-farmer, farm-dashboard)
• installs cifs-utils, go, go-farmer, shinyproxy
• runs go-farmer (go-farmer.service systemd service)
• writes shinyproxy configuration (terraform/shinyproxy.yml)

Initialisation (needed only once)

To initialise terraform prepare a config file config.s3.tfbackend with your s3 credentials:

access_key = "your-access-key"
secret_key = "your-secret-key"
endpoints  = {
        s3 = "https://your-host-base"
}

Ensure your user has access to a s3 bucket and execute

terraform init -backend-config="config.s3.tfbackend"

Now download openrc.sh file for your OpenStack tenant.

Deploy

Prepare a config file config.yaml based on config-template.yaml. Now prepare a file terraform/terraform.tfvars based on terraform-template.tfvars where farm_config would point to your config.yaml. Now execute

cd ./terraform
source openrc.sh
terraform apply

Terraform will now update infrastructure according to main.tf.

You can manage different deployments by changing terraform workspaces. You have to use different OpenStack tenants for each deployment.

Update application on the server

Build and push to Docker Hub a new image. Go to the shinyproxy web-page and launch the app. Shinyproxy will spawn a new container in the background from the new image. Close the app. The old container will die in a minute.