#!/bin/bash
# retrieve DIR_PIPELINE
DIR_PIPELINE=${DIR_PIPELINE=../..}
[[ -f ../.setup.sh ]] && source ../.setup.sh

# setup nr of threads
N=0
[[ $# -eq 1 ]] && N=$1
printf "%d" "$N" >& /dev/null || { echo "error: given nr of threads must be an integer"; exit 255; }
export NTHREADS="$N"

# setup mapping
#$DIR_PIPELINE/bin/setup_orthomapper.sh default_config.sh force
export MAP_ORTHODB_DATA="./data"
export BUSCO_DATA=/tmp/odb_busco
mkdir -p $MAP_ORTHODB_DATA
mkdir -p $BUSCO_DATA
$DIR_PIPELINE/bin/setup.sh


