PJ Steiner:Manatee

some notes on installing Manatee on CSAIL Debian (basically etch)

Mostly based on: http://wiki.nodalpoint.org/manatee_hacks

Manatee: http://manatee.sourceforge.net/

Apache2

at the bottom of /etc/apache2/apache2.conf:

 DocumentRoot "/var/www/html"
 setenv WEBSERVER_TMP /tmp
 ScriptAlias /cgi-bin/ "/var/www/cgi-bin/"
 ScriptAlias /tigr-scripts/ "/var/www/cgi-bin/"
 Alias /webserver_tmp/ "/tmp/"
 # is this bit necessary?
 <Directory "/tmp">
   Allow from all
 </Directory>

MySQL

set password for root

DON'T get rid of debian-sys-whatever user

Perl

debian packages for everything except Log::Cabin

(need to get IO:Tee from testing)

configure/make/make install

./configure with:

 APACHEBIN=/usr/sbin
 HTTPD=/usr/sbin/apache2
 MYSQLBIN=/usr/bin (it looks for mysql here, not mysqld, not sure why)
 MYSQLD = /usr/sbin/mysqld
 HTTPD_SERVER_CONFIG_FILE=/etc/apache2/apache2.conf
 HTTPD_USER=www-data
 HTTPD_GROUP=www-data
 HTTPD_SCRIPT_HOME=/var/www/cgi-bin (I think this should be equal to the first ScriptAlias entry in apache2.conf)
 HTTPD_DOC_HOME=/var/www/html (I think this should be equal to the first DocumentRoot entry in apache2.conf)

Manatee.conf

lives at /var/www/cgi-bin/prok_manatee/conf/Manatee.conf

changes:

   Prok:Mysql:localhost

   ANNOTATION_DIR=/var/lib/search_data

   GZCAT=/bin/zcat

Installing DB

need egad, common, tchar for everything

put organism db in /var/lib/mysql

put search stuff in /var/lib/search_data (then chown -R www-data:www-data?)

MySQL Permissions

make sure file permissions in /var/lib/mysql are correct

 grant all on dbname.* to user@localhost (identified by "password" if it's a new user);
 grant select on {egad.*, common.*, tchar.*} to user@localhost;