https://github.com/biopython/biopython_docker
Dockerfiles to build Biopython instances
https://github.com/biopython/biopython_docker
Last synced: 8 months ago
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Dockerfiles to build Biopython instances
- Host: GitHub
- URL: https://github.com/biopython/biopython_docker
- Owner: biopython
- License: other
- Created: 2015-03-30T10:46:31.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2016-08-30T02:46:16.000Z (over 9 years ago)
- Last Synced: 2025-04-30T10:02:43.257Z (11 months ago)
- Language: Shell
- Size: 1.12 MB
- Stars: 28
- Watchers: 14
- Forks: 10
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
- License: LICENSE.BSD-3-Clause
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README
Docker containers for Biopython
===============================
.. image:: logo/logo_python_final.png
:scale: 40 %
:align: center
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