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LaminDB Docker

Basic docker container configurations with LaminDB components installed.

Available containers

  • bionty-jupyter: lamindb, Bionty, SQLite, Jupyter Notebook tracking (all local)

    Pull with docker pull ghcr.io/laminlabs/lamin-bionty-jupyter:latest

  • aws-bionty-jupyter-postgres: AWS, Bionty, Jupyter Notebook tracking & Postgres

    Pull with docker pull ghcr.io/laminlabs/lamin-aws-bionty-jupyter-postgres:latest. If you don't have postgres already running, we recommend the setup through docker-compose (see below).

Generally, specific versions of lamindb can be pull by replacing 'latest' with the desired version. For example, docker pull ghcr.io/laminlabs/lamin-bionty-jupyter:0.51.0 will pull version 0.51.0.

Mount Lamin volume

When launching containers directly without docker-compose it is advisable to mount the ~/.lamin directory for persistence with existing configurations.

docker run -v ~/.lamin:/home/jovyan/.lamin ghcr.io/laminlabs/lamin-bionty-jupyter:latest

Build & launch containers with docker-compose

You need to have Docker and docker compose installed on your system.

Choose a configuration, navigate into the corresponding subdirectory of configurations/.

To build the container:

docker compose build

Launch Jupyter Lab:

docker compose up

Components

Jupyter notebooks

We use jupyter/base-notebook.

AWS

Since you might need to access AWS resources when working with a Lamin instance, you will need to pass your AWS credentials to the Docker container via environment variables or your ~/.aws folder.

Plain text

Make sure your ~/.aws/config contains the lamin profile (or you can name it whatever you want, but you will have to update the value in the docker-compose.yml accordingly):

[profile lamin]
region=us-east-1

and your ~/.aws/credentials contains your CLI secrets:

[lamin]
aws_access_key_id = **********
aws_secret_access_key = **********

AWS Vault

Even, better, use AWS Vault to secure your credentials using your system's keystore so there are no plaintext secrets on your file system.

aws-vault add lamin
Enter Access Key Id: ********
Enter Secret Key: ********

If you use AWS Vault (you will be prompted to enter your system password)

aws-vault exec lamin -- docker compose up

Postgres

We can launch a Postgres container for the database component. The data volume is mapped to postgres-data so when you relaunch the containers the data persists.

MinIO

We will then use MinIO as an S3-compatible backend. MinIO isn't working yet. To use the MinIO container we will need to pass the container endpoint to LaminDB. It's commented out in the aws-bionty-jupyter-postgres config.

Binder

Binder

This doesn't set up any postgres or MinIO containers, but does allow one to launch an environment with lamindb pre-installed.