Skip to content
This repository
tag: Generic-Genome…
Fetching contributors…

Cannot retrieve contributors at this time

file 161 lines (113 sloc) 4.964 kb
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161
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 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 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
lincoln.stein@gmail.com
October 2008


--- 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>

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)
Something went wrong with that request. Please try again.