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    gemini load -v /home/user/example/processed/gemini-wrapper/norm_annot_vcf/test2.norm.snpeff.gz \
         -t snpEff \
         /home/user/example/processed/gemini-wrapper/gemini_sqlite/test2.vcf.db


    wait


    #######################################################################
    # Finished Gemini Load Section
    #######################################################################

=head2 Notes on Default Values

BioX::Wrapper::Gemini assumes you have environmental variables set for the SnpEff install ($SNPEFF), reference genome ($REFGENOME).

You can change this with

    gemini-wrapper.pl --ref /path/to/reference.fa --snpeff /path/to/snpeff

If you change the snpeff variable you will probably need to change the snpeff_opt

    gemini-wrapper.pl --snpef_opt "-c /path/to/snpeff/snpEff.config -formatEff -classic GRCh37.75"

The gemini db_load_opts has the default set as " -t snpeff". If you would instead like to load it with "--skip_cadd --cores 3 -t snpeff" look at the following.

    gemini_wrapper.pl --db_load_opts "--skip_cadd --cores 3 -t snpeff"

This can be easily accomplished with environment modules. For more information please refer to the modules documentation. http://modules.sourceforge.net/

For more functional documentation check out the wikipedia page. https://en.wikipedia.org/wiki/Environment_Modules_(software)

For easy install try

    sudo yum install environment-modules

See what the variables are with

env |grep MODULE

You can create a custom module path with

    export MODULEPATH=/path/to/user/modules:$MODULEPATH

=head3 SnpEff Module example

    #%Module1.0#######################################################################
    ## SnpEff modulefile
    ##
    proc ModulesHelp { } {

            puts stderr "\tAdds the snpeff binaries to your path.\n module load snpeff \n java -jar $SNPEFF/snpEff.jar -c /path/to/configuration/file/snpEff.config <args>"
    }

    module-whatis   "Adds the snpeff binaries to your path."

    module add java/jdk1.7.0_67

    set ROOT_DIR    /system/apps/software
    setenv  SNPEFF  $ROOT_DIR/snpEff

    #For analysis and denormalizing
    module add samtools/1.2
    prepend-path    PATH    $ROOT_DIR/vt

=head2 Upcoming Functionality

Add in a VEP workflow option

=head1 AUTHOR

Jillian Rowe E<lt>jillian.e.rowe@gmail.comE<gt>

=head1 ACKNOWLEDGEMENTS

This module was originally developed at and for Weill Cornell Medical College in Qatar. With approval from WCMC-Q, this information was generalized and put on github, for which the authors would like to express their gratitude.