Updating WormMart

Overview

WormMart is built every 5 releases of AceDB. Currently, the machine ls2.res.oicr.on.ca is used to build WormMart, then it is moved to the production WormMart machine, wb-biomart.oicr.on.ca.

Databases

Get AceDB

Get the version of AceDB you wish you build WormMart for onto ls2.res.oicr.on.ca

$ cd ~/acedb
$ wget -r -nH --cut-dirs=2 \
  "ftp://ftp.sanger.ac.uk/pub/wormbase/WS${WB_RELEASE}
$ cd WS${WB_RELEASE}
$ ./INSTALL
$ cd ~/acedb
$ rm elegans
$ ln -s WS${WB_RELEASE}/acedb elegans

Start the Ace server

The server is started by calling the saceserver binary as follows ;

$ cd ~/acedb/bin
$ ./saceserver ../elegans 23100 600000:600000:100000 &

Create an empty target WormMart database

$ mysql> create database wormmart_${WB_RELEASE};

Running the Build

On the ls2.res.oicr.on.ca machine:

$ cd $HOME/mart-build/scripts/wormbase-mart

Check the settings at the start of the wormmart_build script

$ <editor> launch_wormmart_build_serial.sh

specifically: WORMMART_DBNAME=wormmart_${WB_RELEASE}

And start the process

$ ./launch_wormmart_build_serial.sh >> WS${WB_RELEASE}.log 2>&1 &

Wait. And hope everything goes well.

Add meta tables

$ cd $HOME/mart-build/scripts/wormbase-mart/wormmart_WS195_meta_tables

load all these tables into the wormmart_${WB_RELEASE} database

Move WormMart to wb-biomart

• test run on ls2.res.oicr.on.ca:9002
• mysqldump and tarball datbase
• copy to wb-biomart
• untar and load

Update Production WormMart

• update /usr/local/wormmart-live/conf/myRegistry.xml / wormMartRegistry.xml

configure new martview

$ cd /usr/local/wormmart-live
$ sudo perl bin/configure.pl -r conf/wormMartRegistry.xml --clean
$ cp conf/httpd.conf.bak conf/httpd.conf

stop old instance of martview

$ kill `cat logs/httpd.pid`

start new instance of martview

$ sudo /usr/local/apache2/bin/apachectl -d /usr/local/wormmart-live -f conf/httpd.conf