Containers

To aid in reproducibility, each work-module in serratus is containerized by job.

Production Containers and Code

## Container Image Hierarchy
# serratus-base
# |    |--serratus-dl
# |    |--serratus-align
# |    |     |--...
# |    |--serratus-merge
# serratus-scheduler
# serratus-grafana
# serratus-prometheus

Building containers

# Start docker service on amazon linux 2
sudo yum install -y docker
sudo yum install -y git
sudo service docker start

# Download latest serratus repo
git clone https://github.com/ababaian/serratus.git; cd serratus/containers

# If you want to upload containers to your repository, include this.
export DOCKERHUB_USER='serratusbio' # optional
sudo docker login # optional

# Build all containers and upload them docker hub repo (if available)
./build_containers.sh

Run interactive an serratus-dl

sudo docker run --rm --entrypoint /bin/bash -it serratus-align:latest

Uploading container images to AWS ECR (Deprecated)

Paste resulting command in terminal to authenticate (not implemented)

## NOTE: Depricated. Jeff builds to dockerhub directly
##       these instructions are for 
#aws ecr get-login --region us-east-1 --no-include-email

## Tag images with ECR information
# sudo docker tag serratus-base:latest 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-base
# sudo docker tag serratus-dl:latest 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-dl
# sudo docker tag serratus-align:latest 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-align
# sudo docker tag serratus-merge:latest 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-merge

## Push images to ECR (rather host on dockerhub)
## Make sure to initialize each repository on your AWS ECR account
# sudo docker push 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-base
# sudo docker push 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-dl
# sudo docker push 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-align
# sudo docker push 797308887321.dkr.ecr.us-east-1.amazonaws.com/serratus-merge

Testing scheduler

cd serratus/scheduler
sudo docker build -t scheduler:0 .
docker run -d --rm -p8000:8000 --name sch scheduler:0
curl -T /path/to/SraRunInfo.csv localhost:8000/add_sra_run_info