The following commands will grab the columns of a config file, using the SLURM_ARRAY_ID to index individual SLiMulations

rep=$(expr $SLURM_ARRAY_ID + 1)

#  An awk 1-liner to grab rows from a set of config files

line=$(awk -v r=$rep 'NR==r {print; exit}' configs )

read -r REP  MAP1  MAP2  NE  SIGA  VS MIG <<< "$line"

Making environments for SLiMulations

Running the following script generates a set of environments for running SLiM simulations.

python buildEnvironments.py

Then run the simulations on your favourite server...

Fill in details here from ComputeCanada...

Run GWAS analysis on simulated data...

First thing to do is to extract a sample of individuals out from the simulated populations...

# make a directory to store the results for each simulation...

parallel "python ../../../bin/sampleFromPopulation.py --tree ../../StochasticMapSLiMulations/{}_1_15.trees -i 1000 -o rep_{}/{}_1000inds" ::: $(seq 1 200)

comedy - tragedy = time