Difference between revisions of "GO installation"

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(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...")
 
(+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
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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”)
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=== Notes ===
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#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.
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#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

  1. 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.
  2. Lucene indexes should be created separately for installed GO. See Lucene indexes creation for details.
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