ILRI Research Computing

1. Install prerequisites http://gmod.org/wiki/GBrowse_2.0_Prerequisites

sudo perl -MCPAN -e 'install Math::BigInt::Pari'
sudo perl -MCPAN -e 'install Digest::SHA'
sudo perl -MCPAN -e 'install Crypt::SSLeay'
sudo perl -MCPAN -e 'install Net::OpenID::Consumer'
sudo perl -MCPAN -e 'install Net::SMTP::SSL'
sudo perl -MCPAN -e 'install Authen::SASL'

2.Install automatically using CPAN shell

$sudo perl -MCPAN -e 'install Bio::Graphics::Browser2'
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Directory for GBrowse's config and support files? [/etc/gbrowse2] 
Directory for GBrowse's static images & HTML files? [/var/www/html/gbrowse2] 
Directory for GBrowse's temporary data [/var/tmp/gbrowse2] 
Directory for GBrowse's sessions, uploaded tracks and other persistent data [/var/lib/gbrowse2] 
Directory for GBrowse's example databases [/var/lib/gbrowse2/databases] 
Directory for GBrowse's CGI script executables? [/var/www/cgi-bin/gb2] 
Internet port to run demo web site on (for demo)? [8000] 
Apache loadable module directory (for demo)? [/etc/httpd/modules] 

3.Edit the following lines in /etc/gbrowse2/GBrowse.conf

65 upload_db_adaptor = DBI::mysql
66 upload_db_host    = localhost
67 upload_db_user    = gbrowse
68 upload_db_pass    = secret

4. Create gbrowse user in mysql

GRANT USAGE ON *.* TO 'gbrowse'@'localhost' IDENTIFIED BY PASSWORD 'secret' 
GRANT ALL PRIVILEGES ON `userdata\_%`.* TO 'gbrowse'@'localhost'                                               
GRANT ALL PRIVILEGES ON `gbrowse_login`.* TO 'gbrowse'@'localhost'                                             
GRANT ALL PRIVILEGES ON `gbrowse_login`.`gbrowse_login` TO 'gbrowse'@'localhost'

5. Create gbrowse user

sudo -u apache gbrowse_create_account.pl gbrowse

New password for gbrowse: 
New password for gbrowse (confirm): 
Enter user's full name (optional): 
Enter user's email address (optional): i.kahugu@cgiar.org
Account "gbrowse": password successfully set.

6. Load Meta data to db

/usr/bin/gbrowse_metadb_config.pl -admin gbrowse:secret

7. Set admin account

gbrowse_set_admin_passwd.pl 

8. Setup email forwarding

Edit the necessary lines on /etc/gbrowse2/GBrowse.conf For now we are authenticating against gmail.com. Later we may use local mail server.

191 # here are some common options
192 # smtp_gateway         = localhost                                 # localhost has properly configured outgoing gateway
193 #smtp_gateway         = 172.26.0.222                        # indicated machine will forward email for you
194 smtp_gateway         = smtp.gmail.com:465:ssl:gbrowsehpc:secret   # use gmail with account "joe.user" and password "secret"
195 # smtp_gateway         = none                                      # disable outgoing email
196 #smtp_gateway           = none  # disable outgoing email
197 
198 # These values are used in the login confirmation message sent during
199 # user registration. You may customize
200 application_name       = GBrowse
201 application_name_long  = The Generic Genome Browser
202 email_address          = gbrowsehpc@gmail.com

9. Start gbrowse

http://hpc.ilri.cgiar.org/gbrowse2/