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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). ******* WARNING ****** The HEAD of SVN (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" svn branch: 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 ---------------------+---------- 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 To install in a custom location, pass the --install_base argument: perl Build.PL --install_base=/home/fred/software 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@example.com April 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 <firstname.lastname@example.org> Ben Faga <email@example.com> Vsevolod (Simon) Ilyushchenko <firstname.lastname@example.org> Marc Logghe <Marc.Logghe@devgen.com> Aaron Mackey <email@example.com> Sheldon McKay <firstname.lastname@example.org> Nathan O. Siemers <Nathan.Siemers@bms.com> Ian Davies <email@example.com> Lincoln Stein <firstname.lastname@example.org> Peter Ruzanov <email@example.com> Special thanks go to the authors of the translations, who include: Franck Aniere <firstname.lastname@example.org> (French) Nansheng Chen <email@example.com> (Chinese) Toshiaki Katayama <firstname.lastname@example.org> (Japanese) Marc Logghe <email@example.com> (Dutch) Marco Mangone <firstname.lastname@example.org> (Italian) Linus Taejoon Kwon <linusben <at> bawi <dot> org> (Korean) Marcela Tello-Ruiz <email@example.com> (Spanish) Gudmundur Thorisson <firstname.lastname@example.org> (Icelandic)