init

#!/bin/bash
#  initialization script.

base=$(dirname $0)
DJZ_ROOT=$(readlink -f $base 2>/dev/null)
case "$1" in
    -d)
        DJZ_APPS="$DJZ_ROOT/apps.testing/"
        DJZ_GENOMES="$DJZ_ROOT/genomes.testing/"
        DJZ_ELMLOGDIR="$DJZ_ROOT/elm-logs.testing/"
        ;;
    *) 
        DJZ_APPS="$DJZ_ROOT/apps/"
        DJZ_GENOMES="$DJZ_ROOT/genomes/"
        DJZ_ELMLOGDIR="$DJZ_ROOT/elm-logs/"
        ;;
esac

for d in $DJZ_APPS $DJZ_GENOMES $DJZ_ELMLOGDIR; do
	test -d $d || echo "WARN: $d does not exist" 1>&2
done
echo "export DJZ_ROOT=\"$DJZ_ROOT\";"
echo "export DJZ_APPS=\"$DJZ_APPS\";"
echo "export DJZ_GENOMES=\"$DJZ_GENOMES\";"
echo "export DJZ_ELMLOGDIR=\"$DJZ_ELMLOGDIR\";"
echo "export PERL5LIB=\"/mnt/software/lib/perl5/5.10.1${PERL5LIB:+:${PERL5LIB}}\";" 
# No doket is used 
#echo "eval $($DJZ_APPS/dotkit080521/init -b);"
#echo "export DK_NODE=\"$DJZ_APPS/dotkit-djz\";"