Test Run Using Demo Data and Demo Yaml File

Run HAPPI GWAS for the first time

The Demo_GLM.yaml, Demo_FarmCPU.yaml, demo dataset, and reference files are provided. Those files are sitting in the repository you cloned into your machine. First, we run HAPPI GWAS with Demo_GLM.yaml.

# Run this in terminal
cd /path/to/HAPPI_GWAS/HAPPI.GWAS
Rscript HAPPI_GWAS.R -GAPIT -extractHaplotype -searchGenes Demo_GLM.yaml

When it is complete, users can find the output files in /path/to/HAPPI_GWAS/output/demo_output_GLM.

Next, we run HAPPI GWAS with Demo_FarmCPU.yaml.

# Run this in terminal
cd /path/to/HAPPI_GWAS/HAPPI.GWAS
Rscript HAPPI_GWAS.R -GAPIT -extractHaplotype -searchGenes Demo_FarmCPU.yaml

When it is complete, users can find the output files in /path/to/HAPPI_GWAS/output/demo_output_FarmCPU.

** Please refer to user-manual section 4.2 for details of files output from HAPPI GWAS.