GBrowse

GBrowse copied to clipboard

#GBrowse is unsupported.

While we still allow pull requests, please be aware that bugs, including security issues, may not ever be addressed.

GBROWSE README

The Generic Genome Browser (GBrowse) is a simple but highly configurable web-based genome browser. It is a component of the Generic Model Organism Systems Database project (GMOD).

******* DOWNLOADING ******

The 2.X versions are now considered stable. You may download it from CPAN at http://search.cpan.org/~lds/GBrowse/ or get the developer's version via SVN:

Checkout read-only git clone git://github.com/GMOD/GBrowse.git

The older 1.X version is still available for download here:

http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-1.70/Generic-Genome-Browser-1.70.tar.gz/download

or via SVN here:

svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/branches/stable Generic-Genome-Browser

SYNOPSIS:

perl Build.PL ./Build distmeta ./Build test ./Build config ./Build demo (optional) ./Build install (will need to become superuser) ./Build apache_conf

TO INSTALL:

Detailed install and configure instructions are available at http://gmod.org/wiki/GBrowse_2.0_HOWTO and we suggest you follow that. What follows here is a brief synopsis.

1. You will need a bunch of Perl prerequisites:

   Module Version ---------------------+---------- perl 5.008
   Bio::Perl 1.007001 CGI::Session 4.02
   Bio::Graphics 2.09 GD 2.07
   Digest::MD5 any File::Temp any
   IO::String any
   JSON any
   LWP any
   Storable any Statistics::Descriptive any

   The Build script will tell you if you are missing any prerequisites. All of these are available on CPAN (www.cpan.org), or by using the CPAN shell ("perl -MCPAN -e shell").

• If you wish to take advantage of user accounts (which lets users share tracks with each other), you must have:

  Module Version ---------------------+---------- DBI any Net::SMTP any

  -and either- DBD::mysql any -or- DBD::SQLite any

• You should install BioPerl from CPAN (currently version 1.7.1) or, to take advantage of additional features and performance boosts, get a snapshot of the current developer version:

  http://github.com/bioperl/bioperl-live/tarball/master

2. Run the command:

   perl Build.PL

   This will create a script named "Build" in the current directory. If you have downloaded and unpacked, but not installed Bioperl, then you should specify its location using the -I option:

   perl -I /home/fred/build/bioperl-live Build.PL

   To install in a custom location, pass the --install_base (preferred) or --prefix argument (deprecated):

   perl Build.PL --install_base=/home/fred/gbrowse perl Build.PL --prefix=/home/fred/gbrowse

3. Run the command:

   ./Build test

   This will run a series of tests on the distribution. If one or more tests fail please inform the author.

4. Run the command:

   ./Build config

   This will ask you a series of questions about where Apache and its support files are located, and will allow you to choose where to install GBrowse's configuration files.

   If you change your mind and want to reconfigure GBrowse, simply run "./Build reconfig".

5. Run the command:

   ./Build demo

   This will launch configure an instance of Apache to run on a local port and give you the URL for a GBrowse demo database. This allows you to try out the system before you install it.

6. Run the command:

   ./Build install

   You will probably need to be the superuser to do this. If you have "sudo" installed the invocation will be:

      % sudo ./Build install
      [sudo] password for jdoe: *****
   

   Otherwise

      % su
      Password: *****
      # ./Build install
   

7. Run the command:

   ./Build apache_config
   

   This will print out a fragment of an Apache configuration file that contains all the information needed to run GBrowse. Cut and paste this into your system's Apache configuration file and restart the server. Usually you will find GBrowse running at http://localhost/gbrowse2.

Support is available from the discussion groups and mailing lists at www.gmod.org.

Lincoln Stein & the GMOD team [email protected] July 2010

--- COPYRIGHT AND LICENSING ---

Copyright (c) 2002 Cold Spring Harbor Laboratory and University of California, Berkeley Copyright (c) 2010 Ontario Institute for Cancer Research

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text.

--- AUTHORS ---

This project has had many authors. Some of the most prominent are:

Scott Cain [email protected] Ben Faga [email protected] Vsevolod (Simon) Ilyushchenko [email protected] Marc Logghe [email protected] Aaron Mackey [email protected] Sheldon McKay [email protected] Nathan O. Siemers [email protected] Ian Davies [email protected] Lincoln Stein [email protected] Peter Ruzanov [email protected] Chris Vandevelde [email protected] Tony deCatanzaro [email protected] Sukhwinder Lall [email protected] Ahmed Einalem [email protected]

Special thanks go to the authors of the translations, who include:

Franck Aniere [email protected] (French) Nansheng Chen [email protected] (Chinese) Toshiaki Katayama [email protected] (Japanese) Marc Logghe [email protected] (Dutch) Marco Mangone [email protected] (Italian) Linus Taejoon Kwon <linusben bawi org> (Korean) Marcela Tello-Ruiz [email protected] (Spanish) Gudmundur Thorisson [email protected] (Icelandic)