#### running clues for simulation study
#### seth d temple, sdtemple at uw dot edu
#### may 23, 2023

Here are instructions.
You run these after your isweep workflow/simulate/.

1. conda env create -f clues-environment.yaml
2. python coarse-coal.py (see args; put under main experiment directory)
  * Use the same time epochs at in relate files. Too fine runs too slow.
3. bcftools query -l some_vcf | head -n some_number > relate.subsample.txt (under main experiment directory)
  * See clues, relate papers. May only want to do a few hundred.
4. Download clues/ from GitHub and place it somewhere on local.
  * https://github.com/standard-aaron/clues
5. Use linux cp command to replace inference.py in clues/ with that in terminalscripts/.
6. Download Relate software and place it somewhere on local.
  * https://myersgroup.github.io/relate/index.html
7. Update the clues.yaml file to reflect file, folders on local.
  * Very few changes.
8. snakemake all -c1 -n --configfile clues.yaml
  * Do a dry run of snakemake.
9. nohup snakemake all -c1 --configfile clues.yaml --jobs 1 --keep-going --cluster "" &
  * See snakemake documentation to modify options.
