Difference between revisions of "GO installation"
From BioUML platform
Tagir Valeev (Talk | contribs) (Created page with "This page describes how to install Gene onthology database and integrate it with BioUML server or BioUML workbench * Download database dump from GO ftp: <code><nowiki>ftp://f...") |
Tagir Valeev (Talk | contribs) (+MySQL packet size info) |
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| − | This page describes how to install Gene onthology database and integrate it with BioUML server or BioUML workbench | + | 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: <code><nowiki>ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz</nowiki></code> | * Download database dump from GO ftp: <code><nowiki>ftp://ftp.geneontology.org/pub/go/godatabase/archive/full/latest/go_(date)-assocdb-data.gz</nowiki></code> | ||
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** 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). | ** 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”) | * 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. | ||
[[Category:Installation]] | [[Category:Installation]] | ||
Latest revision as of 16:45, 15 July 2013
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”)
[edit] 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.
