Docker containers for Biopython

Here you can find Docker containers that include Biopython.

To install these you will need Docker (https://www.docker.com/) on Linux or Docker Toolbox (https://www.docker.com/products/docker-toolbox) on Windows/Mac.

All containers should include all dependencies which can be installed without licensing/copyright issues.

There are 5 containers available at this time:

• A basic one where you ssh into to use it. No databases included.
• A basic one where you ssh into to use it. With BioSQL.
• One with a Jupyter (IPython Notebook) interface,
• One with a Jupyter (IPython Notebook) interface including a Biopython tutorial.
• One for buildbot integration testing.

For each container there will be 2 versions: for Python 3 and legacy Python 2. For now only Python 3 is available.

Installation and Usage

Basic container

In the basic container, you ssh into it and use it from there.

Python 3:

docker pull biopython/biopython
docker run -t -i biopython/biopython /bin/bash
python3  # inside the container

BioSQL container

Python 3:

docker pull biopython/biopython-sql
docker run -t -i biopython/biopython-sql /bin/bash
python3  # inside the container

Jupyter container

Here you will need to point your browser to localhost:9803 (or 9802 on Python 2).

If you are on boot2docker you need to do an extra port mapping step on your VM

Python 3:

docker pull biopython/biopython-notebook
docker run -p 9803:9803 -t -i biopython/biopython-notebook

Jupyter container with tutorials

Here you will need to point your browser to localhost:9803 (or 9802 on Python 2).

If you are on boot2docker you need to do an extra port mapping step on your VM

Python 3:

docker pull biopython/biopython-tutorial
docker run -p 9803:9803 -t -i biopython/biopython-tutorial

Mount your local directory to Docker (here are are naming it $PWD/scratch, but change it as preferred):

docker run -v $PWD:/scratch -e JUPYTER_UID=$UID -it -p 9803:9803 biopython-notebook

Buildbot version

You only need this if you help with our testing effort

You will need to manually download the Docker file and update

CHANGEUSER CHANGEPASS

to your buildbot username and password

Python 3:

#do this in an empty directory
wget https://raw.githubusercontent.com/biopython/biopython_docker/master/biopython-buildbot/Dockerfile
#REMEMBER TO CHANGE CHANGEUSER AND CHANGEPASS
docker build -t biopython-buildbot .
docker run -t -i biopython-buildbot

LICENSING

The software herein is made available under a dual license under the Biopython historic license (see file LICENSE.Biopython) and the 3-clause BSD license (see file LICENSE.BSD-3-Clause)

Logo credits and copyright: Vincent Davis

Authors: Tiago Antao and Tao Zhang with help from Björn Grüning