Difference between revisions of "Updating WormMart"
From WormBaseWiki
Jump to navigationJump to search(7 intermediate revisions by one other user not shown) | |||
Line 14: | Line 14: | ||
$ cd WS${WB_RELEASE} | $ cd WS${WB_RELEASE} | ||
$ ./INSTALL | $ ./INSTALL | ||
+ | $ cd ~/acedb | ||
+ | $ rm elegans | ||
+ | $ ln -s WS${WB_RELEASE}/acedb elegans | ||
=== Start the Ace server === | === Start the Ace server === | ||
The server is started by calling the saceserver binary as follows ; | The server is started by calling the saceserver binary as follows ; | ||
− | $ cd ~/acedb | + | $ cd ~/acedb/bin |
− | |||
− | |||
− | |||
$ ./saceserver ../elegans 23100 600000:600000:100000 & | $ ./saceserver ../elegans 23100 600000:600000:100000 & | ||
Line 34: | Line 34: | ||
Check the settings at the start of the wormmart_build script | Check the settings at the start of the wormmart_build script | ||
− | $ <editor> | + | $ <editor> launch_wormmart_build_serial.sh |
+ | |||
+ | specifically: WORMMART_DBNAME=wormmart_${WB_RELEASE} | ||
And start the process | And start the process | ||
$ ./launch_wormmart_build_serial.sh >> WS${WB_RELEASE}.log 2>&1 & | $ ./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 == | == 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 Production WormMart == | ||
Line 55: | Line 70: | ||
start new instance of martview | start new instance of martview | ||
$ sudo /usr/local/apache2/bin/apachectl -d /usr/local/wormmart-live -f conf/httpd.conf | $ sudo /usr/local/apache2/bin/apachectl -d /usr/local/wormmart-live -f conf/httpd.conf | ||
+ | |||
+ | |||
+ | |||
+ | [[Category:Developer documentation]] |
Latest revision as of 18:24, 17 August 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 $ 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