Genie Requirements

How to execute Genie

Genie was written in Java 1.6. Please make sure Java 1.6 is installed on your Java virtual machine. Download the Java Archive file - Genie.zip from our download page. Add Genie.jar and genepi.jar to your CLASSPATH. Then set up a .rgen parameter file with all the required information. Together with the genotype data file, you can execute Genie as :
java -jar Genie.jar analysis_option [.rgenfile].rgen
If you are running the Quantitative test, a Trait file must be included in the .rgen parameter file, with sub-element datafile and attribute of quantitative and the directory path and file name as the variable.
If you want to run a haplotype analysis, in the .rgen file the top attribute should equal "HapFreqTopSim". A frequency file must be included in the .rgen parameter file, with sub-element datafile and attribute of haplotype and the directory path and file name as the varible.
If you want to use the GeneCounterTopSim simulation option, from GeneCountAlleles program, in the .rgen file the top attribute should specify "GeneCounterTopSim". A linkage parameter loci data file must be specify in the .rgen parameter file, with sub-element datafile and attribute of linkageparameter and the directory path and file name as the variable.
Java 1.6 Java 1.6 installed on your Java virtual machine
Genie.jar This Java Archive file bundles all Genie's class files into a single archive file for easy access.
genepi.jar This Java archive file bundles all Alun Thomas's packages into a single archive file for easy access.
.rgen parameter file XML file defines parameters
pedigree file Linkage pre-makeped pedigree file
trait file Trait / Covariate data file
linkage loci parameter file Linkage loci data desrciption file
Frequency file User defined Haplotype or Allele frequency file
To ensure proper installation of Genie, please download all example files and test run Genie prior to executing your own data. Compare your results with the provided output files. If your result is different from the provided example output, or you encountered errors when running the software, please check your Java 1.6 installation and re-download all Genie files.
Run Output file
java -jar Genie.jar PedGenie SingleLocus.rgen SingleLocus.report
java -jar Genie.jar PedGenie SingleGeneCount.rgen SingleGeneCount.report
java -jar Genie.jar PedGenie CompositeGenotype.rgen PedGenieCompGenotype.report
java -jar Genie.jar PedGenie Haplotype.rgen Haplotype.report

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