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Introduction

IGB supports search using Lucene indexes.

Use the Lucene indexing code (see tools/Lucene) to create indexes for individual data files or all the data files in a directory. The indexes should be stored in IGBQuickLoad directories along with the data files they are indexing.

Lucene indexes are most useful for enabling search of data files such as EST or probe set alignment files that users don't normally load into memory.

Build Lucene.zip

  1. Build Lucene.zip. Define environment variable IGB_WORKDIR, point it to your copy of checked out genoviz trunk or branch
  2. Move full_dist/Lucene.zip to a new directory.
  3. Unzip Lucene.zip. A bunch of new files will appear in the directory with Lucene.zip, including a build.xml file with a target named index that specifies how to build an index.

Specify fields to be indexed by file type

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

Example)

Specific the index target using shell variable optional

Set shell variable lucene_index_dir to specific index source, which can be a single file or a directory. If the source is a directory, then all the files in that directory will be indexed.

Index target file(s)

Run ant using build.xml that was packaged within Lucene.zip.

Examples)

Make indexes for Arabidopsis ATH1 and AG array:

Make indexes for Arabidopsis EST alignments:

Deploy the indexes

The indexes will appear in the same directory as the source files. They do not need to be moved unless they need to be transferred onto a server.

path to index a file or all the files in a directory.
To index one file:

To test

Create indexes locally in a QL site and then add the local QL site to IGB. Do a search using the Advanced Search tab keyword search.

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