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pipeline.sh
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pipeline.sh
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#!/bin/bash
settings=$1
# checks if the job directory is provided
if [[ ! -z $2 ]]
then
#creates directory from argument
mkdir -p $2
cd $2
else
#creates a tmp directory
mkdir -p tmp
cd tmp
fi
#parse settings for get_seq.sh
echo "Running get_seq.sh"
../parse_settings.sh ../$settings get_seq.sh
#parse settings for make_align.sh
echo "Running make_align.sh"
../parse_settings.sh ../$settings make_align.sh
#parse settings for make_phylo.sh
echo "Running make_phylo.sh"
../parse_settings.sh ../$settings make_phylo.sh
#parse settings for make_mol_stats.py
echo "Running make_mol_stats.py"
../parse_settings.sh ../$settings make_mol_stats.py
#parse settings for make_dnds.py
echo "Running make_dnds.py"
../parse_settings.sh ../$settings make_dnds.py
#parse settings for get_hydrophobic_image.py
echo "Running get_hydrophobic_image.py"
../parse_settings.sh ../$settings get_hydrophobic_image.py
#parse settings for generate_hydrophilicity_curve.py
echo "Running generate_hydrophilicity_curve.py"
../parse_settings.sh ../$settings generate_hydrophilicity_curve.py
#parse settings for make_results.py
echo "Runngin make_results.py"
../parse_settings.sh ../$settings make_results.py