feat: Add AutoACMG variables to env.tpl #158

	name: CI

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	Lint:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Run YAML linting
	uses: ibiqlik/action-yamllint@v3
	with:
	file_or_dir: \|
	*.yml
	.github/workflows/*.yml

	- name: Setup linting environment
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: environment.yml
	init-shell: bash
	cache-environment: true
	post-cleanup: none # breaks otherwise

	- name: Check formating
	run: \|
	make ci
	shell: bash -el {0}


	Up-Down:
	runs-on: ubuntu-latest
	needs: Lint
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Prepare secrets
	run: \|
	mkdir -p .ci/secrets
	echo db-password > .ci/secrets/db-password
	echo pgadmin-password > .ci/secrets/pgadmin-password

	- name: Prepare empty volumes
	run: \|
	mkdir -p .ci/volumes/minio/data
	mkdir -p .ci/volumes/pgadmin/data
	mkdir -p .ci/volumes/postgres/data
	mkdir -p .ci/volumes/rabbitmq/data
	mkdir -p .ci/volumes/redis/data
	mkdir -p .ci/volumes/reev-static/data
	mkdir -p .ci/volumes/seqrepo/local
	mkdir -p .ci/volumes/seqrepo/master

	- name: Prepare configuration
	run: \|
	cp .env.ci .env

	mkdir -p .ci/config/nginx
	cp utils/nginx/nginx.conf .ci/config/nginx
	mkdir -p .ci/config/pgadmin
	cp utils/pgadmin/servers.json .ci/config/pgadmin

	- name: Bring up and shut down services
	uses: isbang/[email protected]
	with:
	compose-file: docker-compose.yml
	compose-flags: \|
	--env-file .env
	env:
	DB_PASSWORD: "password"

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