Adding apptainer support (#28)

* Added .gitignore and README
* Updated README for formatting
* Adding apptainer scripts

---------

Co-authored-by: Marc Cummings <[email protected]>

Author: kiwimarc

apptainer/.gitignore

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+*.img
+*.sif

apptainer/README.md

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+# Apptainer for ezBIDS
+
+This guide provides steps to convert Docker containers into Apptainer images and run them efficiently.
+
+## Converting Docker to Apptainer
+
+### Step 1: Build and Stop Docker Containers
+Run the following command to build and start the Docker containers:
+```sh
+docker-compose up --build
+```
+
+Once the containers are running, stop them with:
+```sh
+docker-compose down
+```
+
+### Step 2: Export Docker Images
+Save the running images to `.tar` files:
+```sh
+docker save -o api_image.tar brainlife_ezbids-api
+docker save -o handler_image.tar brainlife_ezbids-handler
+docker save -o ui_image.tar brainlife_ezbids-ui
+docker save -o telemetry_image.tar brainlife_ezbids-telemetry
+```
+For more information, refer to the Docker documentation: [Docker Save Command](https://docs.docker.com/reference/cli/docker/image/save/)
+
+### Step 3: Convert Docker Images to Apptainer Images
+Use the following commands to convert each exported Docker image to an Apptainer `.sif` image:
+```sh
+apptainer build api.sif docker-archive:api_image.tar
+apptainer build handler.sif docker-archive:handler_image.tar
+apptainer build ui.sif docker-archive:ui_image.tar
+apptainer build telemetry.sif docker-archive:telemetry_image.tar
+```
+
+## Usage
+
+### Starting the Containers
+Run the following command to start the Apptainer containers:
+```sh
+./run_apptainer.sh
+```
+
+### Stopping the Containers
+To stop the Apptainer containers, execute:
+```sh
+./stop_apptainer.sh
+```

apptainer/dev_apptainer.sh

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+#!/usr/bin/env bash
+
+cd ..
+
+set -ex
+
+# Parse arguments for authentication flag
+BRAINLIFE_AUTHENTICATION=true
+while getopts "d" flag; do
+ case $flag in
+   d)
+     BRAINLIFE_AUTHENTICATION=false
+   ;;
+   \?)
+   ;;
+ esac
+done
+
+export BRAINLIFE_AUTHENTICATION
+
+# Update git submodules
+git submodule update --init --recursive
+
+# Install dependencies for api and ui
+(cd api && npm install)
+(cd ui && npm install)
+
+# Create necessary directories
+mkdir -p /tmp/upload
+mkdir -p /tmp/workdir
+
+# Prepare husky (if using it for git hooks)
+npm run prepare-husky
+
+# Generate keys (assuming this is a necessary setup step)
+./generate_keys.sh
+

apptainer/mongo_host

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+127.0.0.1 localhost mongodb

apptainer/run_apptainer.sh

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+#!/usr/bin/env bash
+
+./dev_apptainer.sh
+
+if [ ! -e "mongodb.sif" ]; then
+    apptainer build mongodb.sif docker://mongo:4.4.15
+fi
+
+if [ ! -e "api_overlay.img" ]; then
+    apptainer overlay create api_overlay.img
+fi
+
+# Maybe not needed?
+# Does the handler create data else where than tmp?
+if [ ! -e "handler_overlay.img" ]; then
+    apptainer overlay create handler_overlay.img
+fi
+
+if [ ! -e "mongo_overlay.img" ]; then
+    apptainer overlay create mongo_overlay.img
+fi
+
+# Start MongoDB container
+echo "Starting MongoDB container..."
+apptainer instance run --hostname mongodb --overlay mongo_overlay.img mongodb.sif mongodb ./start_mongodb.sh
+
+# Wait for MongoDB to be ready
+echo "Waiting for MongoDB to be ready..."
+sleep 10  # Adjust this based on your needs (or add a health check here)
+
+# Start the API container
+echo "Starting API container..."
+apptainer instance run --overlay api_overlay.img --no-mount /etc/hosts --bind mongo_host:/etc/hosts api.sif api ./start_api.sh
+
+# Wait for API to be ready
+echo "Waiting for API to be ready..."
+sleep 5  # Adjust based on your setup
+
+# Start the Handler container
+echo "Starting Handler container..."
+apptainer instance run --overlay handler_overlay.img --no-mount /etc/hosts --bind mongo_host:/etc/hosts handler.sif handler ./start_handler.sh
+
+# Wait for Handler to be ready (optional)
+echo "Waiting for Handler to be ready..."
+sleep 5  # Adjust as needed
+
+# Start the UI container
+echo "Starting UI container..."
+apptainer instance run --env "VITE_APIHOST=http://localhost:8082"  ui.sif ui ./start_ui.sh
+
+# Start Telemetry container (if in development profile)
+if [ "$PROFILE" == "development" ]; then
+    echo "Starting Telemetry container..."
+    apptainer instance run telemetry.sif telementry ./start_telementry.sh
+fi
+
+# Inform user that containers are running
+echo "All containers are running"

apptainer/start_api.sh

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+#!/usr/bin/env bash
+
+cd ..
+cd api/
+./dev.sh

apptainer/start_handler.sh

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+#!/usr/bin/env bash
+
+cd ..
+cd handler/
+pm2 start handler.js --attach --watch --ignore-watch "ui **/node_modules"

apptainer/start_mongodb.sh

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+#!/usr/bin/env bash
+
+mongod --dbpath /data/

apptainer/start_telementry.sh

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+#!/usr/bin/env bash
+
+cd ..
+cd telementry/
+npm start

apptainer/start_ui.sh

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+#!/usr/bin/env bash
+
+cd ..
+cd ui/
+npm run dev