User Tools

Site Tools


installing_gbrowse2

Differences

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

Link to this comparison view

Next revision
Previous revision
installing_gbrowse2 [2012/02/14 13:49] – created 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_gbrowse2.1329227387.txt.gz · Last modified: 2012/02/14 13:49 by ikahugu