Getting BioPerl

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[edit] BioPerl Packages

[edit] 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 developer 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.

[edit] Bioperl 1.5.2, Developer Release

This represents the latest code 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)

[edit] Bioperl 1.4.0, Stable Release

This release represents that last release from the stable branch released Dec-2003.

Core modules tar.gz zip bz2
Run modules tar.gz zip bz2
C extension modules tar.gz zip bz2

[edit] Other ways to get the releases

[edit] All Releases

http://bioperl.org/DIST Checksums

[edit] Mirrors

iubio.bio.indiana.edu - Daily updates.

[edit] 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.

[edit] Subversion

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

Or, you can browse our anonymous Subversion server.

[edit] Nightly Builds

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

[edit] Installation

[edit] 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.

[edit] 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 Template:Tutorial

[edit] Platform-Specific Instructions

[edit] 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 1.5.1, Developer Release: 

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

For the BioPerl 1.4.0, Stable Release: 

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

For the BioPerl-run 1.5.1, Developer Release: 

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

For the BioPerl-run 1.4.0, Stable 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 1: The ports system prevents you from installing both releases (stable & developer) in the same machine (as they put files in the same locations).

Note 2: If you choose to install any of the BioPerl-run releases, these will check for the installation of their corresponding version of the core package. If versions doesn't match, the install process will fail. If the core package isn't present in the system, it will be automatically fetched and installed.

[edit] 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.

[edit] MacOS 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. To learn more about installing and using fink read this and this.

The stable release of BioPerl (1.4) is available for Mac OS X 10.3 and higher through the so-called 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 or 586.

Recent developer releases of BioPerl are currently only 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 package maintainer. Currently version 1.5.2 is available for Mac OS X 10.4 and 10.5. You can read more about the unstable tree of fink here.

To install the developer release of BioPerl, issue the following command: 

# fink install bioperl-pmXXX

Where XXX is the perl version that is installed on your system, eg 586 or 588. Also the most recent Run package can be installed: 

# fink install bioperl-run-pmXXX
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