Running and Verifying kmersGWAS

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following commands to set the environment variables:

   export PATH=/path/to/KMERSGWAS/kmersGWAS-0.2-beta/bin:$PATH
   export PATH=/path/to/R/bin:$PATH
   export LD_LIBRARY_PATH=/path/to/OPENBLAS/lib:$LD_LIBRARY_PATH

3. Run the following commands to go to the directory for storing test cases, decompress the test cases, and move them to the specified directory:

   cd /path/to/CASE
   tar -zxf A_thaliana_1001G_kmers_table.tar.gz
   mv A_thaliana_1001G_kmers_table /path/to/KMERSGWAS/kmersGWAS-0.2-beta/examples/flowering_time_arabidopsis/

4. Run the following command to go to the directory of test cases:

   cd /path/to/KMERSGWAS/kmersGWAS-0.2-beta/examples/flowering_time_arabidopsis/

5. Run the following command to run the test case:

   { time python2.7 ../../kmers_gwas.py --pheno FT10.pheno --kmers_table A_thaliana_1001G_kmers_table/kmers_table -l 31 -p 128 --outdir run_GWAS_FT10_kp_`date '+%Y%m%d%H%M%S'`; } 2>&1 | tee -a `hostname`_`date '+%Y%m%d%H%M%S'`.log

   Figure 1 shows an example of the running result.

   Figure 1 Result example