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?  Allow from all 

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;