GO installation
From BioUML platform
Revision as of 16:45, 15 July 2013 by Tagir Valeev (Talk | contribs)
This page describes how to install or update Gene onthology database and integrate it with BioUML server or BioUML workbench.
- Download database dump from GO ftp:
ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz - Go to BioUML src directory/db_setup/GO
- Edit build.xml there:
- INPUT_DIRECTORY: where DB dump is located
- FILE_NAME: name of DB dump
- TARGET_PATH: $SERVER_PATH/repo
- DB_HOST, USER, PASS, DATABASE: mysql database to install into (will drop any existing database with the same name and recreate it; make sure that USER/PASS has all privileges to that database).
- Run ant (with default target “install”)
Notes
- You may experience the problems with mysql packet size. See http://dev.mysql.com/doc/refman/5.0/en/packet-too-large.html for details.
- Lucene indexes should be created separately for installed GO. See Lucene indexes creation for details.
