build.sh

#!/bin/bash
set -euo pipefail

source='git@github.com:MRCIEU/'

# ensure we're up to date
git pull

function setup {
	cd ../
	echo $1
	container=$1
	if [ -d "$container" ]; then
		cd $container
		git pull
	else
		git clone --recurse-submodules $source$container.git
		cd $container
	fi
	hash=$(git rev-parse HEAD)
	echo "$hash"
	if [ "$container" == "mrbase-report-module" ]; then
		docker build --no-cache -f ./env/Dockerfile -t "$container":"$hash" .
	else
		docker build --no-cache -t "$container":"$hash" .
	fi
	cd ../igd-api
}

# build latest api image
docker build --no-cache -t mr-base-api-v3:latest .

# build cromwell container with Docker exec
docker build --no-cache -t cromwell-docker ./app/resources/workflow

# build pipeline components
for container in "igd-elasticsearch" "gwas2vcf" "gwas_processing" "mrbase-report-module"
do
	setup $container
done