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= Current Release - 1.59 - 25 February 2011 =
+
= Current Release - 1.64 - 29 May 2014 =
  
 
See also [https://github.com/biopython/biopython/raw/master/NEWS What's new].
 
See also [https://github.com/biopython/biopython/raw/master/NEWS What's new].
Line 5: Line 5:
 
=== Files ===
 
=== Files ===
  
* [http://biopython.org/DIST/biopython-1.59.tar.gz biopython-1.59.tar.gz] 8,377 Kb -- Source Tarball
+
====1.64====
* [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
+
  
Please report any issues on our [[mailing lists]] or [http://redmine.open-bio.org/projects/biopython bug tracker].
+
* [http://biopython.org/DIST/biopython-1.64.tar.gz biopython-1.64.tar.gz] 12Mb -- Source Tarball
 +
* [http://biopython.org/DIST/biopython-1.64.zip biopython-1.64.zip] 13Mb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.64.win32-py2.6.exe biopython-1.64.win32-py2.6.exe] 2Mb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.8.1
 +
* [http://biopython.org/DIST/biopython-1.64.win32-py2.7.exe biopython-1.64.win32-py2.7.exe] 2Mb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.8.1
 +
* [http://biopython.org/DIST/biopython-1.64.win32-py3.3.exe biopython-1.64.win32-py3.3.exe] 2Mb -- 32 bit Windows Installer for Python 3.3 and NumPy 1.8.1
 +
* [http://biopython.org/DIST/biopython-1.64.win32-py3.4.exe biopython-1.64.win32-py3.4.exe] 2Mb -- 32 bit Windows Installer for Python 3.4 and NumPy 1.8.1
 +
 
 +
Please report any issues on our [[mailing lists]] or [https://github.com/biopython/biopython/issues?state=open 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
Line 19: Line 22:
 
=== Installation Instructions ===
 
=== 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).
+
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). For Lion, just get install XCode from the Apple App Store.
+
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 commands:
 
+
Otherwise you typically install from source by downloading and uncompressing the archive, then running the commands:
+
  
 
  python setup.py build
 
  python setup.py build
 
  python setup.py test
 
  python setup.py test
 
  sudo python setup.py install
 
  sudo python setup.py install
 +
 +
Substitute python with your specific version, for example python3, jython or pypy.
 +
 +
For '''Mac OS X''', we recommend installing from source as above. You will need to have installed Apple's XCode tools from the App Store (it is a big download), and then the optional command line tools from within the XCode GUI's options menu, or on Mavericks by using the command:
 +
 +
xcode-select --install
  
 
If you have trouble, see the full installation instructions:
 
If you have trouble, see the full installation instructions:
Line 40: Line 45:
 
=== Required Software ===
 
=== Required Software ===
  
* [http://www.python.org Python 2.4, 2.5, 2.6 or 2.7] (Biopython 1.50 was the last release of Biopython to support Python 2.3)
+
* [http://www.python.org Python 2.5, 2.6, 2.7, 3.3 or 3.4] (Biopython 1.62 is our last release to officially support Python 2.5)
* [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, you should install Apple's XCode ''including'' the command line tools.
* [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 ===
 
For compiling Biopython:
 
* [http://flex.sourceforge.net/ flex: The Fast Lexical Analyzer] -- for building Bio.PDB.mmCIF.MMCIFlex which is used to parse macromolecular Crystallographic Information Files (mmCIF)
 
  
 
Some parts of Biopython use the following additional python libraries:
 
Some parts of Biopython use the following additional python libraries:
 
* [http://www.reportlab.org/downloads.html ReportLab] -- used for pdf graphics code
 
* [http://www.reportlab.org/downloads.html ReportLab] -- used for pdf graphics code
* [http://sourceforge.net/projects/mysql-python MySQLdb] -- used for [[BioSQL]] with a MySQL database
+
* [http://initd.org/psycopg/ psycopg] -- used for [[BioSQL]] with a PostgreSQL database
 +
* [http://dev.mysql.com/downloads/connector/python/ mysql-connector] -- used for [[BioSQL]] with a MySQL database
 +
* [http://sourceforge.net/projects/mysql-python MySQLdb] -- An alternative MySQL library used by [[BioSQL]]
  
 
In addition Biopython includes wrapper code for calling a number of third party command line tools including:
 
In addition Biopython includes wrapper code for calling a number of third party command line tools including:
Line 65: Line 69:
 
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 =
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  sudo apt-get build-dep python-biopython
 
  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.
+
 
 +
=== Archlinux ===
 +
 
 +
Biopython is in the [https://www.archlinux.org/packages/?q=biopython official Archlinux repository] as python-biopython (for Python 3) or python2-biopython (for Python 2) and can be installed using pacman:
 +
 
 +
  pacman -S python2-biopython
 +
 
 +
Or, for Python 3:
 +
 
 +
  pacman -S python-biopython
 +
 
  
 
=== Fedora ===
 
=== Fedora ===
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Recent releases of Biopython require NumPy (and not Numeric):
 
Recent releases of Biopython require NumPy (and not Numeric):
 +
 +
* [http://biopython.org/DIST/biopython-1.63.tar.gz biopython-1.63.tar.gz] 11Mb -- Source Tarball
 +
* [http://biopython.org/DIST/biopython-1.63.zip biopython-1.63.zip] 12Mb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.63.win32-py2.6.exe biopython-1.63.win32-py2.6.exe] 2Mb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.7
 +
* [http://biopython.org/DIST/biopython-1.63.win32-py2.7.exe biopython-1.63.win32-py2.7.exe] 2Mb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.7
 +
* [http://biopython.org/DIST/biopython-1.63.win32-py3.3.exe biopython-1.63.win32-py3.3.exe] 2Mb -- 32 bit Windows Installer for Python 3.3 and NumPy 1.7
 +
 +
* [http://biopython.org/DIST/biopython-1.62b.tar.gz biopython-1.62b.tar.gz] 10,658 Kb -- Source Tarball (''beta release'', 15 July 2013)
 +
* [http://biopython.org/DIST/biopython-1.62b.zip biopython-1.62b.zip] 11,607 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.62b.win32-py2.5.exe biopython-1.62b.win32-py2.5.exe] 1,661 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.62b.win32-py2.6.exe biopython-1.62b.win32-py2.6.exe] 1,686 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.62b.win32-py2.7.exe biopython-1.62b.win32-py2.7.exe] 1,813 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
* [http://biopython.org/DIST/biopython-1.62b.win32-py3.3.exe biopython-1.62b.win32-py3.3.exe] 1,814 Kb -- 32 bit Windows Installer for Python 3.3 and NumPy 1.7
 +
 +
* [http://biopython.org/DIST/biopython-1.61.tar.gz biopython-1.61.tar.gz] 10,311 Kb -- Source Tarball (5 February 2013)
 +
* [http://biopython.org/DIST/biopython-1.61.zip biopython-1.61.zip] 11,198 Kb -- Source Zip File
 +
* [http://biopython.org/DIST/biopython-1.61.win32-py2.5.exe biopython-1.61.win32-py2.5.exe] 1,612 Kb -- 32 bit Windows Installer for Python 2.5 and NumPy 1.1
 +
* [http://biopython.org/DIST/biopython-1.61.win32-py2.6.exe biopython-1.61.win32-py2.6.exe] 1,637 Kb -- 32 bit Windows Installer for Python 2.6 and NumPy 1.3
 +
* [http://biopython.org/DIST/biopython-1.61.win32-py2.7.exe biopython-1.61.win32-py2.7.exe] 1,764 Kb -- 32 bit Windows Installer for Python 2.7 and NumPy 1.5
 +
* [http://biopython.org/DIST/biopython-1.61.win32-py3.2-beta.exe biopython-1.61.win32-py3.2-beta.exe] 1,757 Kb -- 32 bit Windows Installer for Python 3.2 and NumPy 1.5 (''beta'' status for testing)
 +
* [http://biopython.org/DIST/biopython-1.61.win32-py3.3-beta.exe biopython-1.61.win32-py3.3-beta.exe] 1,750 Kb -- 32 bit Windows Installer for Python 3.3 and NumPy 1.7 (''beta'' status for testing)
 +
 +
* [http://biopython.org/DIST/biopython-1.60.tar.gz biopython-1.60.tar.gz] 9,280 Kb -- Source Tarball (25 June 2012)
 +
* [http://biopython.org/DIST/biopython-1.60.zip biopython-1.60.zip] 10,051 Kb -- Source Zip File
 +
* [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-1.60.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-1.60.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
 +
* [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)
 +
 +
* [http://biopython.org/DIST/biopython-1.59.tar.gz biopython-1.59.tar.gz] 8,377 Kb -- Source Tarball (24 February 2012)
 +
* [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.tar.gz biopython-1.58.tar.gz] 7,847 Kb -- Source Tarball (18 August 2011)
Line 134: Line 186:
 
* [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-py2.6.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-1.58.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.tar.gz biopython-1.57.tar.gz] 6,783 Kb -- Source Tarball (2 April 2011)

Latest revision as of 13:49, 29 May 2014

Contents

Current Release - 1.64 - 29 May 2014

See also What's new.

Files

1.64

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. 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

Substitute python with your specific version, for example python3, jython or pypy.

For Mac OS X, we recommend installing from source as above. You will need to have installed Apple's XCode tools from the App Store (it is a big download), and then the optional command line tools from within the XCode GUI's options menu, or on Mavericks by using the command:

xcode-select --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, 2.7, 3.3 or 3.4 (Biopython 1.62 is our last release to officially support Python 2.5)
  • 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, you should install Apple's XCode including the command line tools.
  • 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

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


Archlinux

Biopython is in the official Archlinux repository as python-biopython (for Python 3) or python2-biopython (for Python 2) and can be installed using pacman:

  pacman -S python2-biopython

Or, for Python 3:

  pacman -S python-biopython


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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