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Contents

Current Release -- 1.48 -- 8 September 2008

See also What's new.

Files

Installation Instructions

For Windows we provide click-and-run installers (specific to your version of python), but you will first need to install some prerequisite software (listed below).

Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.

Otherwise you typically install from source by downloading and uncompressing the archive, then running the command:

sudo python setup.py install

If you have trouble, or want to run the test suite, see the full installation instructions:

If you are still stuck, sign up to the Biopython mailing list and ask for help there.

Required Software

Optional Software

Easy Install

If you have easy_install installed on your computer, you can download and install the latest biopython distribution by simply executing this command:

easy_install -f http://biopython.org/DIST/ biopython

You will have to have administrator's rights to do this. Eventually, on a Gnu/Linux system, you could use one of the followings:

sudo easy_install -f http://biopython.org/DIST/ biopython

or

su -; easy_install -f http://biopython.org/DIST/ biopython


Packages

For those of you using Linux, the easiest way to install Biopython is through your distribution's package management system. However, unless you are running a recent release of your Linux Distribution, you may find that the Biopython packages available to be a little out of date. You might want to see if there is a backport available, otherwise you will have to install Biopython from source.

Ubuntu

You should be able to install Biopython and its dependencies using the Synaptic GUI tool (on the main menu under System / Administration / Synaptic Package Manager), or at the command line using:

sudo apt-get install python-biopython

However, this will probably not be the latest release (see listing here). If you want the latest version of Biopython, you will need to install it from source. However, you should be able to automatically install the build dependencies with the following command:

sudo apt-get build-dep python-biopython

Fedora

Biopython is an official Fedora package (since Fedora 5). The package is named python-biopython, and can be installed using yum:

yum install python-biopython

or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later). Biopython 1.45 is the latest available (as of 2008-06-04).

Gentoo Linux

Gentoo's portage tree contains an ebuild (sci-biology/biopython) which builds from source. To install it, open a terminal as root and run:

emerge -va biopython 

Here is a link to Biopython at Gentoo-Portage which shows the latest versions in Gentoo's Portage tree.

Ports

FreeBSD

The most easy way of installing BioPython in FreeBSD is through the Ports Collection. If you're new to this procedure please take a look at this document. Supposing that you're familiar with this method and that you have an up-to-date ports tree, all you need to do is to execute the following commands as root:

# cd /usr/ports/biology/py-biopython
# make install clean

Due to the great architecture of the ports system, this simple commands will automatically fetch and install BioPython (as well as its necessary dependencies).

Old Releases

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