init

#!/bin/bash
dir_scripts="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" # http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in
source $dir_scripts/Utility/utils.sh

# A config file will is needed to tell the init script which files should be analyzed
# and which control file should be used with wach treatment file.
config_file=config.txt

# Reset main directory's Makefile
rm -f Makefile

# Parse configuration file
for treatment in $(cut -f1 $config_file)
do
	# Check if files are valid
	control=$(grep $treatment $config_file | cut -f2 | head -n1)
	check_file $treatment
	check_file $control
	base_treatment=$(basename ${treatment%.*})
	base_control=$(basename ${control%.*})

	# Build directory structure
	dir_treatment=$base_treatment/treatment
	dir_control=$base_treatment/control
	mkdir -p $dir_treatment
	mkdir -p $dir_control

	# Create sub-directory's Makefile
	raw_data_dir=$(dirname $treatment)
	sed_script=$(echo $dir_scripts| sed 's/\//\\\//g')
#	echo "| sed \"s/__SCRIPTS_DIR__/$sed_script/g\" \ "
	cat $dir_scripts/Templates/Makefile_SubDirectories_Template \
	| sed "s/__SCRIPTS_DIR__/$sed_script/g" \
	| sed "s/__TREATMENT_BASE__/$base_treatment/g" \
	| sed "s/__CONTROL_BASE__/$base_control/g" \
	| sed "s/__RAW_DATA_DIR__/$raw_data_dir/g" \
	> $base_treatment/Makefile
# TODO: Should there be a __RAW_DATA_DIR_TREATMENT__ and a __RAW_DATA_DIR_CONTROL__?

	# Add current file to main directory's Makefile
	echo SUBDIRS+=$base_treatment  >> Makefile
done

# Complete the main makefile
echo "" >> Makefile
cat $dir_scripts/Templates/Makefile_MainDirectory_Template >> Makefile