Installing Bioperl on Windows

Contents

 * 1 Introduction
 * 2 Perl Options
 * 3 Installing Perl on Windows
 * 4 CPAN for Strawberry Perl and ActivePerl
 * 5 Bioperl in Cygwin

1 Introduction

This installation guide was written by Barry Moore, Nathan Haigh and other Bioperl authors based on the original work of Paul Boutros. The guide has been updated by Paul Cantalupo and Francisco Ossandon. Note For Windows it is recommended to install BioPerl version 1.6.924 or newer, since many Windows-specific bugs from previous versions were fixed.

Please report problems and/or fixes to the BioPerl mailing list.

2 Perl Options

There are a couple of ways of installing Perl on a Windows machine. One is to get the most recent build from Strawberry Perl and the other is to get it from ActiveState. Both are software companies that provide free builds of Perl for Windows users.

Strawberry Perl is recommended since is more CPAN-friendly and because it includes a compiler (gcc), related tools and other external libraries. These installation steps were verified on December 2015 using ActivePerl 5.20.2.2002 (5.22 has been released but the MinGW package is not available for it yet) and Strawberry Perl 5.22.0.1 from a clean install.

Note Only ActivePerl 5.18 or greater is supported by the BioPerl team. This is because the necessary MinGW package needed for CPAN installations is only available for both 32-bit and 64-bit Windows since this version (32-bit was available on previous versions but only in the Business edition, see ActivePerl MinGW PPM webpage).

Note Support for installation through ActivePerl Perl Package Manager has been dropped in favor of CPAN.

3 Installing Perl on Windows

  1. Download the Strawberry Perl MSI or ActivePerl MSI.
  2. Run the Installer (accepting all defaults is fine).

You can also build Perl yourself (which requires a C compiler). The Perl source for building it yourself is available from CPAN. This approach is not recommended unless you have specific reasons for doing so and know what you’re doing.

Cygwin is a UNIX emulation environment for Windows and comes with its own copy of Perl. Information on Cygwin and Bioperl is found below.

Installation using the ActiveState Perl Package Manager

This installation is not supported nor recommended anymore, because the last BioPerl package produced for it was the old version 1.6.1 (2009) and many Windows-specific bugs were fixed in more recent versions 1.6.923 and 1.6.924. Please install using the CPAN instructions below.

4 CPAN for Strawberry Perl and ActivePerl

Both CPAN and manual methods ultimately need the accessory compiling program MinGW, which incorporates the necessary tools like dmake and gcc. MinGW comes by default with Strawberry Perl, but must it be installed through PPM for ActivePerl (CPAN will display a warning if not present). Also, CPAN need to be upgraded to >= v1.81, Module::Build to be upgraded (>= v0.2805) and Test::Harness to be upgraded to >= v2.62.

Dmake for ActivePerl

1) Install MinGW package through PPM: Using a cmd window type

ppm install MinGW.

It is important to check if ActiveState provides the MinGW package for your ActivePerl version, since each version have to wait its own release. For example, although MinGW has been available since ActivePerl version 5.18, the release for newest version 5.22 it’s still not available (December 2015).

Start the install with CPAN

1) Open a cmd window by going to Start >> Run and typing cmd into the box and pressing return.

2) Type cpan to enter the CPAN shell.

3) At the cpan> prompt, type install CPAN to upgrade to the latest version.

4) Quit (by typing ‘q’) and reload CPAN. You may be asked some configuration questions; accepting defaults is fine.

5) At the cpan> prompt, type o conf prefer_installer MB to tell CPAN to prefer to use Build.PL scripts for installation, and the type o conf commit to save that choice.

6) At the cpan> prompt, type install Module::Build.

7) At the cpan> prompt, type install Test::Harness.

8) At the cpan> prompt, type install Test::Most.

Finish the install with CPAN

You can now follow the instructions INSTALLING BIOPERL THE EASY WAY USING CPAN in the INSTALL file.

Finish the install with BioPerl from GitHub

For the bleeding edge version install manually using a ZIP file from the GitHub repository:

1) Go to GitHub and press the Download ZIP button.

2) Extract the archive in the normal way.

3) In a cmd window cd to the directory you extracted to. Eg. if you extracted to directory ‘bioperl-live’, cd bioperl-live

4) Type perl Build.PL and answer the questions appropriately.

5) Type perl Build test. All the tests should pass, but if they don’t, let us know. Your usage of Bioperl may not be affected by the failure, so you can choose to continue anyway.

6) Type perl Build install to install Bioperl.

5 Bioperl in Cygwin

Cygwin is a Unix emulator and shell environment available free at http://www.cygwin.com. Some users claim that installation of Bioperl is easier within Cygwin than within Windows, but these may be users with UNIX backgrounds. A note on Cygwin: it doesn’t write to your Registry, it doesn’t alter your system or your existing files in any way, it doesn’t create partitions, it simply creates a cygwin/ directory and writes all of its files to that directory. To uninstall Cygwin just delete that directory.

To get Bioperl running first install the basic Cygwin package as well as the Cygwin perl, make, binutils, and gcc packages. Clicking the View button in the upper right of the installer window enables you to see details on the various packages. Then start up Cygwin and follow the Bioperl installation instructions for UNIX in Bioperl’s INSTALL file.

Cygwin paths

If you’re trying to use some application or resource outside of the Cygwin directory and you’re having a problem remember that Cygwin’s path syntax may not be the correct one. Cygwin understands /home/jacky or /cygdrive/e/cygwin/home/jacky (when referring to the E: drive) but the external resource may want E:/cygwin/home/jacky. So your *rc files may end up with paths written in these different syntaxes, depending.

For example, here’s how to set the environmental variable TMPDIR, programs like BLAST and clustalw need a place to create temporary files:

 setenv TMPDIR e:/cygwin/tmp    # csh, tcsh
 export TMPDIR=e:/cygwin/tmp    # sh, bash