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README
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README
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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 1.0069
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 (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 1.6.9) 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
lincoln.stein@gmail.com
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 <cain@cshl.edu>
Ben Faga <benfaga@gmail.com>
Vsevolod (Simon) Ilyushchenko <simonf@cshl.edu>
Marc Logghe <Marc.Logghe@devgen.com>
Aaron Mackey <amackey@pcbi.upenn.edu>
Sheldon McKay <mckays@cshl.edu>
Nathan O. Siemers <Nathan.Siemers@bms.com>
Ian Davies <i.davies2@rogers.com>
Lincoln Stein <lincoln.stein@gmail.com>
Peter Ruzanov <peter.ruzanov@oicr.on.ca>
Chris Vandevelde <Christopher.Vandevelde@oicr.on.ca>
Tony deCatanzaro <tonydecat@gmail.com>
Sukhwinder Lall <sukhwinder.lall@oicr.on.ca>
Ahmed Einalem <aelnaiem@gmail.com>
Special thanks go to the authors of the translations, who include:
Franck Aniere <aniere@genoscope.cns.fr> (French)
Nansheng Chen <chen@cshl.edu> (Chinese)
Toshiaki Katayama <k@bioruby.org> (Japanese)
Marc Logghe <marcl@devgen.com> (Dutch)
Marco Mangone <mangone@cshl.edu> (Italian)
Linus Taejoon Kwon <linusben <at> bawi <dot> org> (Korean)
Marcela Tello-Ruiz <marcela@broad.mit.edu> (Spanish)
Gudmundur Thorisson <mummi@cshl.edu> (Icelandic)