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GBrowse Windows HOWTO

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WARNING

This document has serious issues and installing GBrowse 1.70 on Windows is not easy as a result. Unless you absolutely must use Windows, I suggest you try Linux (as a virtual machine if necessary) instead.

Abstract

This HOWTO describes a method for installing GBrowse version 1.x (currently 1.70) on Windows; GBrowse 2.0 is not supported on Windows.

Windows Installation

Before installing on Windows systems, you will need to install ActiveState Perl and the Apache web server. You may also wish to install a database management system such as MySQL.

Install ActiveState Perl

This may be a show stopper: BioPerl can't be installed in the current releases of ActiveState Perl versions 5.12 and 5.14 because (as far as I know), DB_File can't be installed in those releases. It may be possible to install BioPerl and GBrowse using Strawberry Perl, but I haven't tried.

Go to ActiveState.com, and download the product "ActivePerl." This is a little confusing because web site tries to point you to the commercial product, ASPN Perl. At the current time, the full download URL for ActivePerl is:

http://www.activestate.com/Products/Download/Download.plex?id=ActivePerl

Choose the "MSI" package for Windows for Perl version 5.8. (Version 5.10 does not currently work due to modules that have not yet been made available by ActiveState!) Once downloaded, launch the package, and it will install automatically. Unfortunately, the missing module is DB_File, and is still missing from all post-5.8 releases of ActiveState Perl. I believe it can be installed in ActiveState Perl 5.10 using the Trouchelle repo. I don't know of a similar repo for ActiveState Perl 5.12 or 5.14. It might be possible to install GBrowse with Strawberry Perl, but I haven't tried.

Please accept the default location for ActiveState Perl; this will make it easier to install GBrowse.

Install the Apache web server

Go to http://httpd.apache.org/download.cgi. Select the most recent version of Apache, and choose the download marked "Win32 Binary (MSI Installer)." Once downloaded, launch the package and it will install automatically.

Please accept the default location for Apache.

Install the MySQL database (optional)

Do this only if you want to run the MySQL backend to GBrowse. You might want to wait until after you've played with the flat-file based implementation a bit and decide you need better performance.

Go to http://dev.mysql.com/downloads/mysql. Select and download the most recent version of the Windows package. Once the package is downloaded, you will need to unpack it with the WinZip program. Then launch the installer.

After installing MySQL, install DBD::mysql; the easiest way to do that is via the ActiveState ppm utility.

Install GBrowse and its Perl Dependencies

Download the gbrowse_netinstall.pl script. The script works best when Apache and ActiveState Perl 5.8 are already installed using the default locations. Execute the command in the DOS command shell:

 perl gbrowse_netinstall.pl

And answer questions that are presented (the defaults will be acceptable most of the time, but be careful if you've changed the location of ActiveState and/or Apache!). A few notes:

  • The script requires the LWP Perl package be installed, but it comes by default with ActiveState Perl 5.8.
  • The script also works for Linux and MacOS as long as it is run as root (e.g. with sudo). Please see the GBrowse install doc for more information on what this script is doing.
  • This is out of date, as the bulk loader doesn't yet support pulling GBrowse from git. If you want to use the -d, --bioperl_dev, or --gbrowse_dev options (to install from SVN), you must have a Subversion client installed, such as TortoiseSVN or RapidSVN or xp tweaks

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