Everything you need to deploy this example app is available here: https://github.com/biolib/example-prediction-app

How to deploy an app on Biolib.com in 5 minutes

Every time you run an app on Biolib.com, we spin up a Docker container containing the app on our servers. This container contains the exact program and environment you've specified as a developer, making the app highly reproducible. And infinitely scaleable!

So, how do you deploy an app on Biolib.com?

Requirements:

• Install Docker: https://docs.docker.com/get-docker/
• Install pybiolib: pip3 install -U pybiolib

Step 1: Create your prediction app (this one counts Alanines in a FASTA file)

# Download this example repository
git clone https://github.com/biolib/example-prediction-app
cd example-prediction-app

# Install requirements
pip install -r requirements.txt

# Test that the app works!
python predict.py --fasta sample.fasta --outfile predictions.fasta

Step 2: Create your Dockerfile, build and test it

# (We've already done this - but you can use 'docker init' in the future)
cat Dockerfile

# Build image from Dockerfile in this directory, with tag "prediction-app"
docker build . --platform linux/amd64 -t prediction-app

# Run the image as a container, and start a shell within it
docker run -it prediction-app /bin/bash
# OR
bash dev.sh

# Now test your app inside the container!
python predict.py --fasta sample.fasta --outfile predictions.fasta

Step 3: Create your .biolib/config.yml file, and deploy your image on Biolib.com

# (We've already done this - but you can use 'biolib init' in the future)
cat .biolib/config.yml

# Next we create a new app on Biolib.com
https://biolib.com/new/

# I've used the name prediction-app, found here:
https://biolib.com/BioLibDevelopment/prediction-app

# Before we push, we need to setup an API token (so Biolib knows who we are)
https://biolib.com/settings/api-tokens/

# Set it as an environment variable
export BIOLIB_TOKEN=[your_api_token]

# Everything OK? Let's push the app!
biolib push BioLibDevelopment/prediction-app

# Now check it out on Biolib.com!
https://biolib.com/BioLibDevelopment/prediction-app/

Overview of files

├── README.md               # This file
├── Dockerfile              # How we build the Docker image (everything you need, code-wise)
├── .biolib
│   └── config.yml          # How Biolib interacts with the image 
├── predict.py              # Prediction script
├── sample.fasta            # Example input file
├── predictions.csv         # Example output file
├── requirements.txt        # Dependencies (installed with pip)
├── LICENSE                 # Optional, app license

Read more:

• Building applications guide: https://biolib.com/docs/building-applications/intro/
• .biolig/config.yml guide: https://biolib.com/docs/building-applications/syntax-of-config-yml/
• Dockerfile documentation: https://docs.docker.com/reference/dockerfile/
• How does Docker work? https://www.youtube.com/watch?app=desktop&v=IxzwNa-xuIo

Development tips

Docker tips:

• Dockerfile: Start with "slow" things, and put files you're likely to change last. Docker caches your build in layers, making quick script changes very quick to rebuild if they're in the last layers.
• Dockerfile: Often using base images like ubuntu:22.04 (CPU) or nvidia/cuda:12.0.0-devel-ubuntu22.04 (GPU) is easiest for development. Biolib automatically caches commonly used images for faster loading. If you REALLY care about speed, try using alpine:latest
• Use dev.sh to run the Docker container with an interactive terminal, and bind mount files inside the container (edits files both inside and outside - huge time-saver)
• Suffering from slow Docker build times? Automatically build on our servers every time you git push with our Biolib Pro subscription. Simply modify this Github actions file .github/workflows/ci.yml and put it in your .github/workflows directory.

Biolib tips:

• You can see previously run jobs in the Results tab: https://biolib.com/results/
• You can access your deployed Biolib app with Python. See API examples here: https://biolib.com/docs/using-applications/python/
• .biolig/config.yml - Create a nice app user-interface with these arguments: https://biolib.com/docs/building-applications/syntax-of-config-yml/#arguments
• .biolig/config.yml - Create nice output visualizations using the main_output_file argument (supports HTML, CSV, FASTA, markdown and more.

FAQ

Why use Docker?

• Docker solves the problem of "but it runs on my machine!". A Docker container can run on any machine supporting Docker, can easily be scaled across thousands of jobs, and has an exact, reproducible environment now and 20 years into the future.

What exactly does pybiolib do?

• For our purposes, it finds the Docker image you built (from the tag you specified in .biolig/config.yml) and pushes it to Biolib. It also pushes a few other files if present, including LICENSE, README, images in README, and of course, the .biolib/config.yml file).

It doesn't work!

• Please ask for help in our Biolib community slack (biolibcommunity.slack.com), and we are more than happy to help!