Updating WormMart
From WormBaseWiki
Contents
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
Start the Ace server
The server is started by calling the saceserver binary as follows ;
$ cd ~/acedb/bin $ ./saceserver ../acedb/WS${WB_RELEASE} 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 $ mkdir -p ./logs
Check the settings at the start of the wormmart_build script
$ <editor> launch_wormmart_build.sh
And start the process
$ ./launch_wormmart_build_serial.sh >> WS${WB_RELEASE}.log 2>&1 &