Some of these are for use on an HPC cluster
Usage:
./submitSTR.sh <infile.pbs> <starting_K_value> <last_K_value> <optional: TEST_FLAG>
Infile should be a .pbs script that runs structure on an HPC cluster
example PBS script is included in this Github repository as example.pbs
PBS script MUST HAVE '&' symbol in sed command; it gets replaced with K values
GNU parallel should be used for multiple runs
If you want to use TEST_FLAG, just type any string as the fourth command-line argument If TEST_FLAG is
defined, the script will print to STDOUT instead of submitting to queue
$2 and $3 arguments submit structure runs from K=$2 to K=$3
Output is piped into qsub command unless TEST_FLAG is defined
Usage:
./get-avg-cov_pyradS3.sh s3.clusters_filename outfile
Script takes the s3.clusters.txt output from pyRAD and calculates the average coverage with Depth>N
Usage:
./genPBS.sh <outfile_name_with_extension>
Generates blank PBS file for use on an HPC cluster
Usage: ./process_admixture.sh [arguments]
Use help option to see specific details about required arguments:
./process_admixture.sh -h
Requires two of Steve Mussmann's scripts to work. Run help menu of script to see details.