UPDATE

Here are the list of programs/databases etc that will need to be updated...

1) Ensemble perl script may need to be updated but will have to check manually. The script can be found in ~/galaxy-dist/tools/SOER1000genes/galaxy/ensemblVEP/variant_effect_predictor.pl

2) SnpEff will need to be manually updated also. You will have to visit his site http://snpeff.sourceforge.net/ and check for the latest versions.

Once downloaded unzip into the /home/galaxy/galaxy-dist/tools/SOER1000genes/src/snpEff folder and run the ./setup_snpEff.sh script which will take care of placing the files where they need to be.

To update to the latest reference genome, 
    cd into /home/galaxy/galaxy-dist/tool-data/shared/jars/snpEff/data
and run
    Rm -Rf *
    then run cd .. 
    and run
    java -jar snpEff.jar download latestRefGenome
and it should have installed into the data folder. It may return errors while downloading but chances are that it worked anyway.
    
   If the reference Genome has been updated to a version that did 
   not exist in the previous SnpEff installation a column must be
   added to the /home/galaxy/galaxy-dist/tools/snpEff/snpEff.xml 

   Open up snpEff.xml using a txt editor and navigate to 
   <param name="genomeVersion" ...
 
  and add a <option value="<latestRefGenome>">LaterRefGenome:Homo_sapiens</option>

  This example applies in the case of the updated human reference genome

3) The GATK is sometimes updated (or will be at least) so all that needs to be done is:

    mv GenomeAnalysisTK.jar /home/galaxy/galaxy-dist/tool-data/shared/jars/gatk
    mv *.* (everything but the jar) to /home/galaxy/galaxy-dist/tools/gatk

4) dbSNP will need to be updated as new versions come out. 
You can update dbSNP by running the update_dbSnp.sh script in SOER1000genes/scripts folder:
        sudo ./update_dbSnp.sh