signet

#!/bin/bash

operate=${1}

options=""
for((i=2;i<=$#;i++)); do 
    j=${!i}
    options="${options} $j "
done

#Set directories
cd $(dirname $0)

mkdir -p data
mkdir -p tmp
mkdir -p res

SIGNET_ROOT=$(/bin/pwd)
SIGNET_DATA_ROOT="$SIGNET_ROOT/data"
SIGNET_TMP_ROOT="$SIGNET_ROOT/tmp"
SIGNET_RESULT_ROOT="$SIGNET_ROOT/res"
SIGNET_SCRIPT_ROOT="$SIGNET_ROOT/script"
#echo -n The directory that stores data is:
#echo $SIGNET_DATA_ROOT
#echo -n The directory that stores the temporary files is:
#echo $SIGNET_TMP_ROOT
#echo -n The directory that stores the results is:
#echo $SIGNET_RESULT_ROOT
#echo -n The directory that stores the scripts is:
#echo $SIGNET_SCRIPT_ROOT
export SIGNET_ROOT=$SIGNET_ROOT
export SIGNET_DATA_ROOT=$SIGNET_DATA_ROOT
export SIGNET_TMP_ROOT=$SIGNET_TMP_ROOT
export SIGNET_RESULT_ROOT=$SIGNET_RESULT_ROOT
export SIGNET_SCRIPT_ROOT=$SIGNET_SCRIPT_ROOT

. $SIGNET_SCRIPT_ROOT/file_manage.sh  

geno_prep(){
	$SIGNET_SCRIPT_ROOT/geno_prep_portal.sh ${options};
}

gexp_prep(){
	$SIGNET_SCRIPT_ROOT/gexp_prep_portal.sh ${options};
}


config(){
    $SIGNET_SCRIPT_ROOT/config_controller.sh ${options};
}

network(){
	$SIGNET_SCRIPT_ROOT/network_portal.sh ${options};
}

cis_eqtl(){
	$SIGNET_SCRIPT_ROOT/cis_portal.sh ${options};
}
netvis(){
	$SIGNET_SCRIPT_ROOT/netvis_portal.sh ${options};
}
adj(){
	$SIGNET_SCRIPT_ROOT/adj_portal.sh ${options};
}
echo -e ""


case "$operate" in
    -g|-geno)
        geno_prep;;
    -t|-transcript)
        gexp_prep;;
    -n|-network)
        network;;
    -c|-cis_eqtl)
        cis_eqtl;;
    -s|-settings)
	config;;
    -v|-vis)
	netvis;;
    -a|-adj)
	adj;;
    *)
	if [[ $(which cat) != 0 && -f $SIGNET_SCRIPT_ROOT/logo ]];then 
	cat $SIGNET_SCRIPT_ROOT/logo
        else
	echo -e "WELCOME TO SIGNET !!! \n"
        fi
	echo -e "Usage params: -g|-t|-n|-c|-s|-v|-a"
        ;;
esac        

echo -e ""

exit 0