Getting BioPerl
From BioPerl
Contents |
BioPerl Packages
- Core package provides the main parsers, this is the basic package and it's required by all the other packages (bioperl-live Subversion directory)
- Run package provides wrappers for executing some 60 common bioinformatics applications (bioperl-run in Subversion)
- BioPerl db is a subproject to store sequence and annotation data in a BioSQL relational database (bioperl-db in Subversion).
- Network package parses and analyzes protein-protein interaction data (bioperl-network in Subversion).
- GUI package includes some basic widgets in Perl-Tk (bioperl-gui in Subversion).
- Ext package is for C-language extensions including some alignment algorithms and an interface to the Staden IO library (bioperl-ext in Subversion).
- Pedigree package is for manipulating genotype, marker, and individual data for linkage studies (bioperl-pedigree in Subversion)
- Microarray package has preliminary objects for manipulating some microarray data formats (bioperl-microarray in Subversion)
- Pipeline package is a project for creating analysis pipelines out of bioperl-run modules (bioperl-pipeline in Subversion).
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.
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) |
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 |
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:
- bioperl-live This is the core of BioPerl, and probably what you want.
- bioperl-run
- bioperl-ext
- bioperl-db
- bioperl-network
Or, you can browse our anonymous Subversion server.
Nightly Builds
TO BE ADDED
Installation
Unix
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 1.5.1, 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.
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. 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
