Getting BioPerl

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BioPerl Packages

BioPerl Releases

All current and past distributions are available from the BioPerl Distribution. For more information about the different versions and the stable versus developer distinction please see a related question in the FAQ.

Which version should I get?

  • If you are just starting with Bioperl, you should download the stable release as it is the most currently maintained release.
  • If you have older scripts and are concerned about API compatibility, you may want install the stable Bioperl.

Bioperl 1.6.0, Stable Release

This represents the latest code from the main development base, released Jan-2009. Only core modules have been released for 1.6 at this time, but the accompanying packages (run,network,db) will be released soon after.

Core modules tar.gz zip bz2

Bioperl 1.5.2, Developer Release

This represents the a code release from the main development base, released Dec-2006.

Core modules tar.gz zip bz2
Run modules tar.gz zip bz2
DB modules tar.gz zip bz2
Network modules tar.gz zip bz2
C extension modules tar.gz zip bz2 (from Bioperl 1.5.1)

Other ways to get the releases

All Releases

http://bioperl.org/DIST Checksums

Mirrors

iubio.bio.indiana.edu - Daily updates.

Perl CPAN

http://search.cpan.org/search?dist=bioperl

Information on how to use CPAN.pm to automatically download BioPerl and various CPAN module dependencies is described in our INSTALL file.

Subversion

If you want to live on the edge, learn about using Subversion directly:

Or, you can browse our anonymous Subversion server.

Nightly Builds

See http://www.bioperl.org/DIST/nightly_builds/

Installation

Unix

There are pre-compiled binary packages available for Unix-like systems for some parts of bioperl for Fedora via yum and MacOS X using fink. If you wish to compile from source, first read the installation instructions for all Unix systems in the INSTALL file or on the Bioperl wiki.

Windows

Instructions for Windows can also be found in the INSTALL.WIN file or in the wiki. You may or may not have to download any files from this page, depending on how you choose to install Bioperl. The PPM (*ppm.tar.gz) files for Windows installation can be found at http://bioperl.org/DIST.

Also see the tutorial Installing Perl modules Tutorial

Platform-Specific Instructions

FreeBSD

The most easy way of installing BioPerl 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:

For the BioPerl 1.6.0 Release: 

# cd /usr/ports/biology/p5-bioperl
# make install clean

For the BioPerl-run 1.6.0 Release: 

# cd /usr/ports/biology/p5-bioperl-run
# make install clean

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

Note: If you choose to install the BioPerl-run release, this will check for the installation of the core package. If the core package isn't present in the system, it will be automatically fetched and installed.

Fedora

bioperl (1.5.2) and bioperl-run are official Fedora packages, available in Fedora 7 and later, known as perl-bioperl and perl-bioperl-run, respectively. To install simply run as root: 

# yum install perl-bioperl

This will pull in all the necessary Perl dependencies. Alternatively the package can be installed via GUI package management front-ends, pirut (in F-8) and PackageKit (in F-9 and later), either by searching for bioperl, or browsing the Applications/Engineering group (see Pirut documentation and PackageKit documentation). Other bioperl subpackages such as bioperl-db and bioperl-network are not packaged as of 2008-06-04, but you are welcome to contact Alex Lancaster if you would like to help package or maintain these packages in Fedora.

Mac OS X using fink

Before installing BioPerl on Mac OS X, several other packages and perl modules need to be installed that are required by BioPerl. The fink package manager will make it easy to download and install all the required packages, modules and BioPerl itself. However not all optional prerequisites are available through fink, so some functionality may be not working. To learn more about installing and using fink read this and this.

BioPerl version 1.6.1 is available through the unstable tree in fink. This doesn't mean that this package is unstable, it just means that not many users have tried it and used it, and provided positive feedback to the fink project. You can read more about the unstable tree of fink here. If you are going to install BioPerl from source, you'll first need install the developer tools from Apple. You can obtain these here. If you haven't already, you'll need to register to become an ADC member before you can download the tools. To download the tools (called Xcode), a free membership is sufficient.

To install BioPerl from source, issue the following command: 

# fink install bioperl-pmXXX

Where XXX is the perl version that is installed on your system, eg 586 or 588. Bioperl-Run is also available through fink: 

# fink install bioperl-run-pmXXX

If you don't want to install from source, BioPerl version 1.5.2 is available for Mac OS X 10.4 and higher (10.3 is no longer supported by fink) through the binary distribution of fink and can be installed using the following command: 

# sudo apt-get install bioperl-pmXXX

Where XXX is the perl version that is installed on your system, eg 581, 586 or 588.

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