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1 GBROWSE README
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2
5d018d0 @lstein New release
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3 The Generic Genome Browser (GBrowse) is a simple but highly
4 configurable web-based genome browser. It is a component of the
5 Generic Model Organism Systems Database project (GMOD).
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6
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7 ******* DOWNLOADING ******
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8
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9 The 2.X versions are now considered stable. You may download it from
10 CPAN at http://search.cpan.org/~lds/GBrowse/ or get the developer's
11 version via SVN:
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12
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13 Checkout read-only
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14 git clone git://github.com/GMOD/GBrowse.git
15
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16
17 The older 1.X version is still available for download here:
18
19 http://sourceforge.net/projects/gmod/files/Generic%20Genome%20Browser/GBrowse-1.70/Generic-Genome-Browser-1.70.tar.gz/download
20
21 or via SVN here:
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22
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23 svn co https://gmod.svn.sourceforge.net/svnroot/gmod/Generic-Genome-Browser/branches/stable Generic-Genome-Browser
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24
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25 **************************
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26
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27 SYNOPSIS:
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28
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29 perl Build.PL
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30 ./Build distmeta
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31 ./Build test
32 ./Build config
33 ./Build demo (optional)
34 ./Build install (will need to become superuser)
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35 ./Build apache_conf
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36
37 TO INSTALL:
38
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39 Detailed install and configure instructions are available at
40 http://gmod.org/wiki/GBrowse_2.0_HOWTO and we suggest you follow
41 that. What follows here is a brief synopsis.
42
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43 1) You will need a bunch of Perl prerequisites:
44
45 Module Version
46 ---------------------+----------
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47 perl 5.008
48 Bio::Perl 1.0069
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49 CGI::Session 4.02
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50 Bio::Graphics 2.09
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51 GD 2.07
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52 Digest::MD5 any
53 File::Temp any
54 IO::String any
55 JSON any
56 LWP any
57 Storable any
58 Statistics::Descriptive any
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59
60 The Build script will tell you if you are missing any
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61 prerequisites. All of these are available on CPAN (www.cpan.org),
62 or by using the CPAN shell ("perl -MCPAN -e shell").
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63
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64 - If you wish to take advantage of user accounts (which lets users share
65 tracks with each other), you must have:
66
67 Module Version
68 ---------------------+----------
69 DBI any
70 Net::SMTP any
71
72 -and either-
73 DBD::mysql any
74 -or-
75 DBD::SQLite any
76
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77 - You should install BioPerl from CPAN (currently version 1.6.9) or, to
78 take advantage of additional features and performance boosts, get a
79 snapshot of the current developer version:
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80
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81 http://github.com/bioperl/bioperl-live/tarball/master
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82
83 2) Run the command:
84
85 perl Build.PL
86
87 This will create a script named "Build" in the current directory. If you
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88 have downloaded and unpacked, but not installed Bioperl, then you should
89 specify its location using the -I option:
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90
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91 perl -I /home/fred/build/bioperl-live Build.PL
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92
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93 To install in a custom location, pass the --install_base (preferred) or
94 --prefix argument (deprecated):
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95
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96 perl Build.PL --install_base=/home/fred/gbrowse
97 perl Build.PL --prefix=/home/fred/gbrowse
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98
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99 3) Run the command:
100
101 ./Build test
102
103 This will run a series of tests on the distribution. If one or more tests
104 fail please inform the author.
105
106 4) Run the command:
107
108 ./Build config
109
110 This will ask you a series of questions about where Apache and its support
111 files are located, and will allow you to choose where to install GBrowse's
112 configuration files.
113
114 If you change your mind and want to reconfigure GBrowse, simply run
115 "./Build reconfig".
116
117 5) Run the command:
118
119 ./Build demo
120
121 This will launch configure an instance of Apache to run on a local port and
122 give you the URL for a GBrowse demo database. This allows you to try out the
123 system before you install it.
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124
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125 6) Run the command:
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126
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127 ./Build install
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128
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129 You will probably need to be the superuser to do this. If you have "sudo" installed
130 the invocation will be:
131
132 % sudo ./Build install
133 [sudo] password for jdoe: *****
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134
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135 Otherwise
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136
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137 % su
138 Password: *****
139 # ./Build install
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140
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141 7) Run the command:
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142
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143 ./Build apache_config
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144
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145 This will print out a fragment of an Apache configuration file that contains
146 all the information needed to run GBrowse. Cut and paste this into your system's
147 Apache configuration file and restart the server. Usually you will find GBrowse
148 running at http://localhost/gbrowse2.
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149
150 Support is available from the discussion groups and mailing lists at
151 www.gmod.org.
152
153 Lincoln Stein & the GMOD team
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154 lincoln.stein@gmail.com
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155 July 2010
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156
116976c @lstein 1.38 Mon Apr 8 21:16:12 EDT 2002
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157
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158 --- COPYRIGHT AND LICENSING ---
159
160 Copyright (c) 2002 Cold Spring Harbor Laboratory and University of California, Berkeley
161 Copyright (c) 2010 Ontario Institute for Cancer Research
162
163 This package and its accompanying libraries is free software; you can
164 redistribute it and/or modify it under the terms of the GPL (either
165 version 1, or at your option, any later version) or the Artistic
166 License 2.0. Refer to LICENSE for the full license text.
167
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168 --- AUTHORS ---
169
170 This project has had many authors. Some of the most prominent are:
171
172 Scott Cain <cain@cshl.edu>
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173 Ben Faga <benfaga@gmail.com>
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174 Vsevolod (Simon) Ilyushchenko <simonf@cshl.edu>
175 Marc Logghe <Marc.Logghe@devgen.com>
176 Aaron Mackey <amackey@pcbi.upenn.edu>
cd276a9 Added an application called gbrowse_karyotype. It uses the gbrowse
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177 Sheldon McKay <mckays@cshl.edu>
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178 Nathan O. Siemers <Nathan.Siemers@bms.com>
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179 Ian Davies <i.davies2@rogers.com>
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180 Lincoln Stein <lincoln.stein@gmail.com>
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181 Peter Ruzanov <peter.ruzanov@oicr.on.ca>
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182 Chris Vandevelde <Christopher.Vandevelde@oicr.on.ca>
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183 Tony deCatanzaro <tonydecat@gmail.com>
184 Sukhwinder Lall <sukhwinder.lall@oicr.on.ca>
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185 Ahmed Einalem <aelnaiem@gmail.com>
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186
187 Special thanks go to the authors of the translations, who include:
188
189 Franck Aniere <aniere@genoscope.cns.fr> (French)
190 Nansheng Chen <chen@cshl.edu> (Chinese)
191 Toshiaki Katayama <k@bioruby.org> (Japanese)
192 Marc Logghe <marcl@devgen.com> (Dutch)
193 Marco Mangone <mangone@cshl.edu> (Italian)
194 Linus Taejoon Kwon <linusben <at> bawi <dot> org> (Korean)
195 Marcela Tello-Ruiz <marcela@broad.mit.edu> (Spanish)
196 Gudmundur Thorisson <mummi@cshl.edu> (Icelandic)
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