GO installation

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Revision as of 18:05, 11 June 2013 by Tagir Valeev (Talk | contribs)

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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: 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

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