launch_single_cosi_iteration_local.sh

launch_single_cosi_iteration_local.sh

#!/usr/bin/env bash
# Launch a single cosi iteration.
# 
# Standard usage (to run one single simulation)
#
#   $: ./launch_single_cosi_iteration_local.sh simulation1 data/simulation_output/
#
#
# Description of parameters:
# 
#   $1 -> iteration number (usually I execute 100 iteration for each set of parameters)
#   $2 -> base output folder
#
# It is recommended to execute this script in combination with gnu/parallel.
# The following will launch 100 simulations, in parallel:
# 
#   $: seq 1 100 | parallel -i sh ./launch_single_cosi_iteration_local.sh {} ../../data/neutral_sims
# 
# NOTES:
# 
# each iteration is run in a single directory, defined by $1
# all the files necessary are copied in the directory
# the recombination model is calculated by recosim for each iteration.
## 
 
# 

# 

REPLICA_ID=$1
OUTPUTDIR=$2
#REPLICA_ID=$SGE_TASK_ID
#OUTPUTDIR=../../data/simulations

# Copy all cosi binaries to a temporary subfolder of the output directory
mkdir -p ${OUTPUTDIR}/tmp/${REPLICA_ID}
mkdir -p ${OUTPUTDIR}/param_logs
mkdir -p ${OUTPUTDIR}/results
cp autosomes_deCODE.distr params recParams recosim coalescent ${OUTPUTDIR}/tmp/${REPLICA_ID}
#cp autosomes_deCODE.distr recosim coalescent ${OUTPUTDIR}/${REPLICA_ID}
cp recParams ${OUTPUTDIR}/tmp/${REPLICA_ID}/bestfit_neutral_replica_${REPLICA_ID}
cd ${OUTPUTDIR}/tmp/${REPLICA_ID}

# generate the recombination model (model.test), and run cosi
./recosim bestfit_neutral_replica_${REPLICA_ID} 1000000
./coalescent -p ./params -o ../../results/bestfit_neutral_replica_${REPLICA_ID}
gzip -f ../../results/bestfit_neutral_replica_${REPLICA_ID}.*

# Clean the temporary subfolder, and move all results to output dir
rm coalescent recosim
mv model.test ../../param_logs/bestfit_neutral_replica_rec_${REPLICA_ID}
gzip -f ../../param_logs/bestfit_neutral_replica_rec_${REPLICA_ID}
#rm model.test
#gzip ../../param_logs/bestfit_neutral_replica_decode_${REPLICA_ID}
#mv autosomes_deCODE.distr ../../param_logs/bestfit_neutral_replica_decode_${REPLICA_ID}
rm autosomes_deCODE.distr 
#gzip ../../param_logs/bestfit_neutral_replica_decode_${REPLICA_ID}
#mv recParams ../../param_logs/bestfit_neutral_rec_replica_${REPLICA_ID}
#gzip ../../param_logs/bestfit_neutral_rec_replica_${REPLICA_ID}
rm recParams 
rm params 
rm bestfit_neutral_replica_${REPLICA_ID}

cd ..
rmdir ${REPLICA_ID}
#cd ..
#rmdir ${OUTPUTDIR}