forked from GMOD/GBrowse
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README
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README
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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).
******* WARNING ******
The HEAD of CVS (including this file) is currently in alpha test. You
are encouraged to give this a try, and to report your experiences to
the mailing lists at www.gmod.org.
For production, we suggest you use one of the released tarballs, or
check out the "stable" cvs branch:
cvs -d pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co -r stable Generic-Genome-Browser
**********************
SYNOPSIS:
perl Build.PL
./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
---------------------+----------
Bio::Perl 1.005002
CGI::Session 4.02
Digest::MD5 0
File::Temp 0
GD 2.07
IO::String 0
JSON 0
LWP 0
perl 5.008
Storable 0
The Build script will tell you if you are missing any
prerequisites. With the exception of BioPerl, all of these are
available on CPAN (www.cpan.org), or by using the CPAN shell
("perl -MCPAN -e shell").
- You will need the Bioperl DEVELOPER release (version 1.5.9). It is
quite stable, so you should not need to worry about installing it,
but if you wish, you can set up GBrowse to use a non-installed
version of Bioperl simply by unpacking it in your home directory
or some other convenient location. Download Bioperl here:
http://bioperl.org/DIST/current_core_unstable.tar.gz
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
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
October 2008
--- AUTHORS ---
This project has had many authors. Some of the most prominent are:
Scott Cain <cain@cshl.edu>
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>
Lincoln Stein <lstein@cshl.edu>
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)