ILRI Research Computing

User Tools

Site Tools

You are here: start » installing_gbrowse2
installing_gbrowse2

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
installing_gbrowse2 [2012/02/14 13:50] – ikahuguinstalling_gbrowse2 [2012/02/14 14:12] (current) – ikahugu
Line 1: Line 1:
-1. Install **[[prerequisites]]**+1. Install prerequisites 
 +[[http://gmod.org/wiki/GBrowse_2.0_Prerequisites]] 
 + 
 +<code> 
 +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' 
 +</code> 
 + 
 +2.Install automatically using CPAN shell 
 +<code>$sudo perl -MCPAN -e 'install Bio::Graphics::Browser2' 
 +. 
 +. 
 +. 
 + 
 +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]  
 + 
 + 
 +</code> 
 + 
 + 
 +3.Edit the following lines in /etc/gbrowse2/GBrowse.conf 
 +<code> 
 +65 upload_db_adaptor = DBI::mysql 
 +66 upload_db_host    = localhost 
 +67 upload_db_user    = gbrowse 
 +68 upload_db_pass    = secret</code> 
 + 
 +4. Create gbrowse user in mysql 
 +<code> 
 +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' 
 +</code> 
 + 
 +5. Create gbrowse user 
 +<code> 
 +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. 
 +</code> 
 + 
 +6. Load Meta data to db 
 +<code> 
 +/usr/bin/gbrowse_metadb_config.pl -admin gbrowse:secret 
 +</code> 
 + 
 +7. Set admin account 
 +<code>gbrowse_set_admin_passwd.pl  
 +</code> 
 + 
 +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. 
 +<code> 
 +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 
 + 
 +</code> 
 +9. Start gbrowse 
 +<code> 
 +http://hpc.ilri.cgiar.org/gbrowse2/</code> 
 + 
 + 
 + 
 + 
 + 
  
  
installing_gbrowse2.1329227420.txt.gz · Last modified: 2012/02/14 13:50 by ikahugu