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.
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
Python 3:
docker pull biopython/biopython-sql docker run -t -i biopython/biopython-sql /bin/bash python3 # inside the 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
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
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
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