Website:GBrowse Set-up on dev.wormbase.org

From WormBaseWiki
Jump to: navigation, search

Each user has his/her own installation directory on the development server.

Note: Update yourusername with your username in the following.

Your local WormBase website and GBrowse directory:

/usr/local/wormbase/website/yourusername

Updating/Replacing your GBrowse Installation

Place a GBrowse source copy, e.g. GBrowse v2.54, in a publicly accessible spot such as:

/usr/local/wormbase/website/yourusername/GBrowse-2.54

Generate build and makefiles:

perl Makefile.PL

Generate a config tailored to your user directory, or update the current installation to point to your user directory:

./Build config
# or
./Build reconfig

Answer the interactively prompted questions as follows:

Reuse previous configuration as defaults? [y ]n

**Beginning interactive configuration**
Directory for GBrowse's config and support files? [/etc/gbrowse2] /usr/local/wormbase/website/yourusername/conf/gbrowse
Directory for GBrowse's static images & HTML files? [/var/www/gbrowse2] /usr/local/wormbase/website/yourusername/root/gbrowse
Directory for GBrowse's temporary data [/var/tmp/gbrowse2] /usr/local/wormbase/tmp/gbrowse
Directory for GBrowse's sessions, uploaded tracks and other persistent data [/var/lib/gbrowse2] /usr/local/wormbase/website/yourusername/root/gbrowse/tmp
Directory for GBrowse's example databases [/var/lib/gbrowse2/databases]
Directory for GBrowse's CGI script executables? [/usr/lib/cgi-bin/gb2] /usr/local/wormbase/website/yourusername/root/gbrowse/cgi
Internet port to run demo web site on (for demo)? [8008]
Apache loadable module directory (for demo)? [/usr/lib/apache2/modules]
User account under which Apache daemon runs? [www-data]
Automatically update Apache config files to run GBrowse? [y] n
Automatically update system config files to run gbrowse-slave? [y] n

Build and install GBrowse in your local installation directory:

Note: Ensure that you [K]eep GBrowse conf files in your installation and have them not overwritten. Everything else can be [R]eplaced.

sudo ./Build install

Apache needs to be restarted afterwards, so that the changes come into affect:

sudo apache2ctl restart