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

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 >> WS210_at.log 2>&1 &