== Installation Notes . ==
 * Got mysqldump from Mark.
   * *    *    * $ sudo ./mysqlimport5 -u molgenis -p a.sql > database_test
   * (permission denied!)
 * Fixing error in molgenis new distro (hvp_pilot ) missing molgenis jar files.
 * Just noticed that Molgenis has also common_collections jar file . Maybe conflict with peregrine there .
 * Lucene @ mac :
   * Fix classpath at .profile (Users ~ home directory) :
     * * export CLASSPATH=/Users/despoina/Documents/Lucene/lucene-3.0.1/lucene-core-3.0.1.jar:/Users/despoina/Documents/Lucene/lucene-3.0.1/lucene-demos-3.0.1.jar
   * In order to create an index for a directory ".../path/", run :
     * prompt $ java org.apache.lucene.demo.!IndexFiles /...path/
     * Search the created index by :
       * * prompt: java org.apache.lucene.demo.[wiki:SearchFiles]
     * Locate the database files and create an index on them :
       * Successfully build an index in a.sql dump file of Syndrome book data . Unfortunately when searching a term that exists more that once, only one reference is found ! -->
         * * Enter query:
         * acetylgalactosaminyltransferase
         * Searching for: acetylgalactosaminyltransferase
         * 1 total matching documents
         * 1. /Users/despoina/Documents/SyndromeBookDATA/a.sql
       * So maybe if they are on different tables, or on an xml file !
         * TODO : will try that on the tables of hvp_pilot :
           * TODO : fill some data
             * TODO increase gene_description size.
               * * changed                *                 <field name="geneDescription"  /> TO         <field name="geneDescription" type="text" />
       * TODO : COmmit svn : (problem with javahl    --> chflags -R nouchg .)
         * This problem & solution : http://stackoverflow.com/questions/1765232/subclipse-cant-rename-file-os-x
         * Database changed .
         * Text input inserted .
         * Gene description field from table Gene transformed to Text . (in order to increase size).
       * or ....[http://kalanir.blogspot.com/2008/06/indexing-database-using-apache-lucene.html http://kalanir.blogspot.com/2008/06/indexing-database-using-apache-lucene.html]
 * MYSQL on mac : bins @ /opt/local/var/macports/software/mysql5/5.1.45_0/opt/local/bin
   * dbs @   /opt/local/var/db/mysql5   * *