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the Generic Genome Browser

branch: master

Merge pull request #37 from srobb1/master

added region_label to pass region name on in url--thanks Sofia!
latest commit 3c844ce086
Scott Cain scottcain authored
Octocat-spinner-32 bin Adding some flexibility for parsing alignment meta-data July 22, 2013
Octocat-spinner-32 cgi-bin Merge branch 'master' of July 24, 2013
Octocat-spinner-32 conf added check so that region_label does not get printed if not wanted December 10, 2013
Octocat-spinner-32 contrib fix broken configuration process August 25, 2011
Octocat-spinner-32 debian fix broken configuration process August 25, 2011
Octocat-spinner-32 docs added developer documentation for GBrowse AMI July 12, 2011
Octocat-spinner-32 etc fix log path name January 08, 2013
Octocat-spinner-32 htdocs Merge pull request #29 from edelgadoh/master November 27, 2013
Octocat-spinner-32 install_util fix wrong precedence bug in setting perl5lib July 24, 2013
Octocat-spinner-32 lib Fix failure of feature summary message to appear on mousedown events. August 29, 2013
Octocat-spinner-32 libalign big cleanup of defunct files; migrating to Module::Build October 16, 2008
Octocat-spinner-32 sample_data Truncation-related data corruption resolved August 28, 2012
Octocat-spinner-32 t fix database directory references in tutorial conf files July 09, 2013
Octocat-spinner-32 .cvsignore quench cvs up messages about unknown files July 06, 2009
Octocat-spinner-32 Build.PL updating GD version required July 21, 2013
Octocat-spinner-32 Changes Fix failure of feature summary message to appear on mousedown events. August 29, 2013
Octocat-spinner-32 DISCLAIMER * Implemented a new caching scheme for communicating with renderfarm … May 07, 2010
Octocat-spinner-32 INSTALL updating doc to indicate how out of date it is June 03, 2011
Octocat-spinner-32 LICENSE * Implemented a new caching scheme for communicating with renderfarm … May 07, 2010
Octocat-spinner-32 MANIFEST MIssing toggle.js was breaking gbrowse_syn and a few plugins (need to… July 22, 2013
Octocat-spinner-32 MANIFEST.SKIP Fix "can't call FETCH without object reference" errors during ./Build… September 17, 2012
Octocat-spinner-32 Makefile.PL Fix performance problems when using in-memory databases composed of m… July 10, 2013
Octocat-spinner-32 README add missing credits October 11, 2011
Octocat-spinner-32 README.IF.GBROWSE.ISNT.WORKING updated to indicate this file is out of date - perhaps should be removed April 14, 2013
Octocat-spinner-32 README.fedora_and_selinux added an experimental "fix" for selinux problems November 05, 2008
Octocat-spinner-32 README.gff3 updated GBrowse READMEs with SVN checkout instructions September 15, 2009
Octocat-spinner-32 TODO start working on script to create skeleton db August 21, 2012
Octocat-spinner-32 foobar testing dev branch May 25, 2011

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 or get the developer's
version via SVN:

Checkout read-only
git clone git://

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

or via SVN here:

svn co Generic-Genome-Browser



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


Detailed install and configure instructions are available at 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               1.0069
    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 (,
    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
    DBD::SQLite             any

- You should install BioPerl from CPAN (currently version 1.6.9) or, to
  take advantage of additional features and performance boosts, get a
  snapshot of the current developer version:

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: *****


          % 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

Lincoln Stein & the GMOD team
July 2010


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 <>
Ben Faga <> 
Vsevolod (Simon) Ilyushchenko <>
Marc Logghe <>
Aaron Mackey <>
Sheldon McKay <>
Nathan O. Siemers <>
Ian Davies <>
Lincoln Stein <>
Peter Ruzanov <>
Chris Vandevelde <>
Tony deCatanzaro <>
Sukhwinder Lall <>
Ahmed Einalem <>

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

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