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= Current Release - 1.55 ''beta'' - 18 August 2010 =
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= Current Release - 1.60 - 25 June 2012 =
  
See also [http://biopython.open-bio.org/SRC/biopython/NEWS What's new].
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See also [https://github.com/biopython/biopython/raw/master/NEWS What's new].
  
 
=== Files ===
 
=== Files ===
  
* [http://biopython.org/DIST/biopython-1.55b.tar.gz biopython-1.55b.tar.gz] 6,428 Kb -- Source Tarball
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* [http://biopython.org/DIST/biopython-1.60.tar.gz biopython-1.60.tar.gz] 9,280 Kb -- Source Tarball
* [http://biopython.org/DIST/biopython-1.55b.zip biopython-1.55b.zip] 6,996 Kb -- Source Zip File
+
* [http://biopython.org/DIST/biopython-1.60.zip biopython-1.60.zip] 10,051 Kb -- Source Zip File
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.4.exe biopython-1.55b.win32-py2.4.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
+
* [http://biopython.org/DIST/biopython-1.60.win32-py2.5.exe biopython-1.60.win32-py2.5.exe] 1,469 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.5.exe biopython-1.55b.win32-py2.5.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
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* [http://biopython.org/DIST/biopython-1.60.win32-py2.6.exe biopython-1.60.win32-py2.6.exe] 1,492 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.6.exe biopython-1.55b.win32-py2.6.exe] 1,474 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
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* [http://biopython.org/DIST/biopython-1.60.win32-py2.7.exe biopython-1.60.win32-py2.7.exe] 1,1618 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 
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* [http://biopython.org/DIST/biopython-1.60.win32-py3.2-beta.exe biopython-1.60.win32-py3.2-beta.exe] 1,611 Kb -- 32 bit Windows Installer for Python 3.2 and NumPy 1.5 (''beta'' status for testing)
'''NOTE''' : This is a ''beta'' release for testing. It would be unwise to install this on a production machine without doing extensive testing (instead install Biopython 1.54, links at end of page).
+
  
Please report any issues on our [[mailing lists]] or [http://bugzilla.open-bio.org/ bugzilla].
+
Please report any issues on our [[mailing lists]] or [http://redmine.open-bio.org/projects/biopython bug tracker].
  
 
Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has
 
Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has
 
kindly made [http://www.lfd.uci.edu/~gohlke/pythonlibs/ Windows 64bit installers] for
 
kindly made [http://www.lfd.uci.edu/~gohlke/pythonlibs/ Windows 64bit installers] for
NumPy 1.4.1 and Biopython 1.54 (and other tools) available for testing.
+
NumPy and Biopython (and other tools) available for testing.
  
 
=== Installation Instructions ===
 
=== Installation Instructions ===
Line 25: Line 24:
 
Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.
 
Most Linux distributions will include an optional Biopython package (described below), and will take care of any prerequisite software automatically.
  
For Mac OS X, we recommend installing from source (see below). You will need to have installed Apple's XCode tools ''including'' the optional 10.4 SDK (check the option for 10.4 support when installing Xcode tools).
+
For Mac OS X, we recommend installing from source (see below). Under (Snow) Leopard, you will need to have installed Apple's XCode tools ''including'' the optional 10.4 SDK (check the option for 10.4 support when installing Xcode tools) which comes on DVD with the computer. For Lion, just install XCode from the Apple App Store (it is a big download).
  
 
Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:
 
Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:
Line 42: Line 41:
 
=== Required Software ===
 
=== Required Software ===
  
* [http://www.python.org Python 2.4, 2.5 or 2.6] (Biopython 1.50 was the last release of Biopython to support Python 2.3)
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* [http://www.python.org Python 2.5, 2.6 or 2.7] (Biopython 1.56 was the last release to officially support Python 2.4, although Biopython 1.58 should work)
* [http://www.python.org/doc/current/inst/inst.html C compiler (if compiling from source)] You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms.  This is not needed on Windows if using the install programs provided above. On Mac OS, we recommend you install Apple's XCode ''including'' the 10.4 SDK.
+
* [http://www.python.org/doc/current/inst/inst.html C compiler (if compiling from source)] You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms.  This is not needed on Windows if using the install programs provided above. On Mac OS, we recommend you install Apple's XCode ''including'' the 10.4 SDK if offered.
* [http://numpy.scipy.org/ NumPy (Numerical Python)]. Note that until BioPython 1.49, Biopython used the older Numeric library.  We have tested NumPy 1.0, 1.1, 1.2, and 1.3 with Biopython.
+
* [http://numpy.scipy.org/ NumPy (Numerical Python)]. Note that until Biopython 1.49, Biopython used the older Numeric library.  We have tested NumPy 1.1 to 1.5 with Biopython.
  
 
=== Optional Software ===
 
=== Optional Software ===
Line 67: Line 66:
 
If you have [http://peak.telecommunity.com/DevCenter/EasyInstall easy_install] installed on your computer, you can download and install the latest Biopython distribution by simply executing this command:
 
If you have [http://peak.telecommunity.com/DevCenter/EasyInstall easy_install] installed on your computer, you can download and install the latest Biopython distribution by simply executing this command:
  
 +
<pre>
 
  easy_install -f http://biopython.org/DIST/ biopython
 
  easy_install -f http://biopython.org/DIST/ biopython
 +
</pre>
  
 
You will have to have administrator's rights to do this. On a Unix style system this is normally done by:
 
You will have to have administrator's rights to do this. On a Unix style system this is normally done by:
  
 +
<pre>
 
  sudo easy_install -f http://biopython.org/DIST/ biopython
 
  sudo easy_install -f http://biopython.org/DIST/ biopython
 +
</pre>
  
 
= Packages =
 
= Packages =
Line 130: Line 133:
 
Recent releases of Biopython require NumPy (and not Numeric):
 
Recent releases of Biopython require NumPy (and not Numeric):
  
* [http://biopython.org/DIST/biopython-1.54.tar.gz biopython-1.54.tar.gz] 6,295 Kb -- Source Tarball
+
* [http://biopython.org/DIST/biopython-1.59.tar.gz biopython-1.59.tar.gz] 8,377 Kb -- Source Tarball
 +
* [http://biopython.org/DIST/biopython-1.59.zip biopython-1.59.zip] 9,127 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.59.win32-py2.5.exe biopython-1.59.win32-py2.5.exe] 1,440 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.59.win32-py2.6.exe biopython-1.59.win32-py2.6.exe] 1,463 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.59.win32-py2.7.exe biopython-1.59.win32-py2.7.exe] 1,590 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.58.tar.gz biopython-1.58.tar.gz] 7,847 Kb -- Source Tarball (18 August 2011)
 +
* [http://biopython.org/DIST/biopython-1.58.zip biopython-1.58.zip] 8,474 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.58.win32-py2.4-unsupported.exe biopython-1.58.win32-py2.4-unsupported.exe] 1,427 Kb -- 32 bit Windows Installer for Python 2.4 (which we no longer officially support) and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.58.win32-py2.5.exe biopython-1.58.win32-py2.5.exe] 1,428 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.58.win32-py2.6.exe biopython-1.58.win32-py2.6.exe] 1,450 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.58.win32-py2.7.exe biopython-1.58.win32-py2.7.exe] 1,577 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.57.tar.gz biopython-1.57.tar.gz] 6,783 Kb -- Source Tarball (2 April 2011)
 +
* [http://biopython.org/DIST/biopython-1.57.zip biopython-1.57.zip] 7,446 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.4-unsupported.exe biopython-1.57.win32-py2.4-unsupported.exe] 1,405 Kb -- 32 bit Windows Installer for Python 2.4 (which we no longer officially support) and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.5.exe biopython-1.57.win32-py2.5.exe] 1,405 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.6.exe biopython-1.57.win32-py2.6.exe] 1,428 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.57.win32-py2.7.exe biopython-1.57.win32-py2.7.exe] 1,555 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.56.tar.gz biopython-1.56.tar.gz] 6,778 Kb -- Source Tarball (26 November 2010)
 +
* [http://biopython.org/DIST/biopython-1.56.zip biopython-1.56.zip] 7,347 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.56.win32-py2.4.exe biopython-1.56.win32-py2.4.exe] 1,429 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.56.win32-py2.5.exe biopython-1.56.win32-py2.5.exe] 1,429 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.56.win32-py2.6.exe biopython-1.56.win32-py2.6.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.56.win32-py2.7.exe biopython-1.56.win32-py2.7.exe] 1,578 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.55.tar.gz biopython-1.55.tar.gz] 6,493 Kb -- Source Tarball (31 August 2010)
 +
* [http://biopython.org/DIST/biopython-1.55.zip biopython-1.55.zip] 7,058 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.55.win32-py2.4.exe biopython-1.55.win32-py2.4.exe] 1,448 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.55.win32-py2.5.exe biopython-1.55.win32-py2.5.exe] 1,449 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.55.win32-py2.6.exe biopython-1.55.win32-py2.6.exe] 1,471 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.55.win32-py2.7.exe biopython-1.55.win32-py2.7.exe] 1,598 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
 
 +
* [http://biopython.org/DIST/biopython-1.55b.tar.gz biopython-1.55b.tar.gz] 6,428 Kb -- Source Tarball (August 18, 2010)
 +
* [http://biopython.org/DIST/biopython-1.55b.zip biopython-1.55b.zip] 6,996 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.4.exe biopython-1.55b.win32-py2.4.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.5.exe biopython-1.55b.win32-py2.5.exe] 1,451 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.55b.win32-py2.6.exe biopython-1.55b.win32-py2.6.exe] 1,474 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
 
 +
* [http://biopython.org/DIST/biopython-1.54.tar.gz biopython-1.54.tar.gz] 6,295 Kb -- Source Tarball (May 20, 2010)
 
* [http://biopython.org/DIST/biopython-1.54.zip biopython-1.54.zip] 6,859 Kb -- Source Zip File
 
* [http://biopython.org/DIST/biopython-1.54.zip biopython-1.54.zip] 6,859 Kb -- Source Zip File
 
* [http://biopython.org/DIST/biopython-1.54.win32-py2.4.exe biopython-1.54.win32-py2.4.exe] 1,434 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1
 
* [http://biopython.org/DIST/biopython-1.54.win32-py2.4.exe biopython-1.54.win32-py2.4.exe] 1,434 Kb -- 32 bit Windows Installer for Python 2.4 and NumPy 1.1

Revision as of 18:16, 25 June 2012

Contents

Current Release - 1.60 - 25 June 2012

See also What's new.

Files

Please report any issues on our mailing lists or bug tracker.

Note we don't (yet) have official 64 bit Windows Installers - however, Christoph Gohlke has kindly made Windows 64bit installers for NumPy and Biopython (and other tools) available for testing.

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, in particular, NumPy).

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

For Mac OS X, we recommend installing from source (see below). Under (Snow) Leopard, you will need to have installed Apple's XCode tools including the optional 10.4 SDK (check the option for 10.4 support when installing Xcode tools) which comes on DVD with the computer. For Lion, just install XCode from the Apple App Store (it is a big download).

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

python setup.py build
python setup.py test
sudo python setup.py install

If you have trouble, see the full installation instructions:

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

Required Software

  • Python 2.5, 2.6 or 2.7 (Biopython 1.56 was the last release to officially support Python 2.4, although Biopython 1.58 should work)
  • C compiler (if compiling from source) You need a C compiler supported by distutils, gcc will work fine on UNIX-like platforms. This is not needed on Windows if using the install programs provided above. On Mac OS, we recommend you install Apple's XCode including the 10.4 SDK if offered.
  • NumPy (Numerical Python). Note that until Biopython 1.49, Biopython used the older Numeric library. We have tested NumPy 1.1 to 1.5 with Biopython.

Optional Software

For compiling Biopython:

Some parts of Biopython use the following additional python libraries:

In addition Biopython includes wrapper code for calling a number of third party command line tools including:

  • Wise2 -- for command line tool dnal
  • NCBI Standalone BLAST -- command line tool for running BLAST on your local machine
  • Clustalw -- command line tool for building sequence alignments
  • SIMCOAL2 and FDist -- command line tools for population genetics
  • EMBOSS -- lots of useful command line tools.

Easy Install

We don't officially sanction this option, but it has been reported to work fine. 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. On a Unix style system this is normally done by:

 sudo 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 or Debian

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

If you want the documentation and unit tests,

sudo apt-get install python-biopython-doc

And if you want to use BioSQL,

sudo apt-get install python-biopython-sql

However, this will probably not be the latest release (see Ubuntu listing here, and Debian 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

Note: You may need to additionally install the NumPy package by hand, as a very out of date repository may still expect Biopython to use Numeric instead.

Fedora

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

yum install python-biopython

or via one of the GUI package management systems such as pirut and PackageKit (available in F-9 and later).

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

Recent releases of Biopython require NumPy (and not Numeric):

Please note that Biopython 1.48 and older require the Numeric library, not its replacement NumPy. Windows installers for Python 2.4 and older are available from the Numerical Python website. A Windows installer for Numeric 24.2 for Python 2.5 is available here: Numeric-24.2.win32-py2.5.exe 446 Kb

Please note that Biopython 1.48 and older used mxTextTools 2.0 in some of the parsers. There were a few niggles with mxTextTools 3.0, so ideally install the older mxTextTools 2.0.

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