Genie Requirements¶
- How to execute Genie
Genie is written in Java. Please make sure Java is installed. Download and unpack the archive file - Genie.zip - from gitlab. 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 installed on your Java virtual machine
Genie.zip
This archive available from gitlab
This Java archive file bundles all Alun Thomas’s packages into a single archive file for easy access.
XML file defines parameters
Linkage pre-makeped pedigree file
Trait / Covariate data file
Linkage loci data desrciption 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
java -jar Genie.jar PedGenie SingleGeneCount.rgen
java -jar Genie.jar PedGenie CompositeGenotype.rgen
java -jar Genie.jar PedGenie Haplotype.rgen