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run_step.sh
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run_step.sh
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#!/bin/bash
###############################################################################
# Aydin Karatas
# Project Coprolite Viromes
# run_step.sh
###############################################################################
cd $HOME/project_coprolite_viromes
script=$1
filename=$(basename "$script")
if [[ $filename =~ ^[0-9]+_ ]]; then
# run pal samples
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pal-AWC
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pal-BEL
./run_ori.sh -s $script -d 8 -c 16 -p $SCRATCH/project_coprolite_viromes -o pal-BMS
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pal-ENG
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pal-ZAF
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pal-ZAP
# run ind samples
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o ind-DNK
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o ind-ESP
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o ind-USA
# run non-ind samples
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pre-FJI
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pre-MDG
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pre-MEX
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pre-PER
./run_ori.sh -s $script -d 8 -c 8 -p $SCRATCH/project_coprolite_viromes -o pre-TZA
elif [[ $filename =~ ^[0-9]+a_ ]]; then
# run auxilliar script that is not specific to an origin
./run_ori.sh -s $script -d 8 -c 4 -p $SCRATCH/project_coprolite_viromes -o all
fi