Difference between revisions of "Updating WormMart"
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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. | 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. | ||
| − | == Get AceDB == | + | == Databases == |
| + | |||
| + | === Get AceDB === | ||
Get the version of AceDB you wish you build WormMart for onto ls2.res.oicr.on.ca | Get the version of AceDB you wish you build WormMart for onto ls2.res.oicr.on.ca | ||
| Line 12: | Line 14: | ||
$ cd WS${WB_RELEASE} | $ cd WS${WB_RELEASE} | ||
$ ./INSTALL | $ ./INSTALL | ||
| + | |||
| + | === Start the Ace server === | ||
| + | The server is started by calling the saceserver binary as follows ; | ||
| + | $ saceserver $DBDIR/WS${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.sh | ||
Revision as of 18:28, 24 June 2010
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 ;
$ saceserver $DBDIR/WS${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.sh
