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the Generic Genome Browser
PSGI aws-slave-grow-vol berkeley-gadfly bigwig_gff_prep branch-1_47 cnvandev database_not_found development faceted-searching fix-authentication-issues gbrowse-session-template gbrowse-session gbrowse-template-branch idavies_gbrowse-common_branch_20090615 idavies_gbrowse_common_base_20090617 imagemap_pull lstein master nliles_gbrowse_circular package-tools pinned-tracks-2 pinned-tracks plack postgres_gbrowse_syn_load_alignments_msa reference-gbrowse-template release-2_09 release-2_17-bugfixes release-2_21 release_1_62-bugfixes release_1_62 sonu2 sonudev2 sonudev3 sonuipaddev stable syn_2x_modules syn_2x test-wig-upload transparency
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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:firstname.lastname@example.org:/cvsroot/gmod login cvs -d :pserver:email@example.com:/cvsroot/gmod co -r 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 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 firstname.lastname@example.org October 2008 --- AUTHORS --- This project has had many authors. Some of the most prominent are: Scott Cain <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> Lincoln Stein <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)