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out of date content - available for reference purposes only

Table of Contents

Introduction

IGB supports search using Lucene indexes starting with IGB release 7.0.

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  1. Define an environment variable IGB_WORKSPACE, which should point to your copy of the checked-out genoviz trunk or branch.
  2. Run ant to compile the code. A new directory named full_dist will appear that contains LuceneIndexing.zip.
  3. Change into the full_dist directory and unzip LuceneIndexing.zip.

Example)

Code Block

export IGB_WORKSPACE=$HOME/src/genoviz/trunk
ant # build the code
cd full_dist
unzip LuceneIndexing.zip

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Currently, to run the indexing code, you'll need a copy of felix.jar that contains a Main class and enables you to launch the OSGi framework. We'll probably change this at some point, but for now, download the latest felix.

Example)

Code Block

wget http://mirrors.gigenet.com/apache//felix/org.apache.felix.main.distribution-4.2.1.tar.gz

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Edit resources/index.properties. Use this file to specify which fields in which file types will be indexed.

Example)

Code Block

_default=id,name,gene name,description
_ignore=method,source,type,seq
psl=id

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Make indexes for Arabidopsis ATH1 and AG array:

Code Block

ant -Dext.lucene_index_dir=$HOME/src/genomes/pub/quickload/A_thaliana_Jun_2009/Affymetrix

Make indexes for Arabidopsis EST alignments:

Code Block

ant -Dext.lucene_index_dir=$HOME/src/genomes/pub/quickload/A_thaliana_Jun_2009/EST

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