#!/usr/bin/env bash
#orthologer - Pipeline for deducing orthology from fasta files.
#
#Copyright (C) 2005-2020 E. Zdobnov lab: F. Tegenfeldt
#<fredrik.tegenfeldt@unige.ch> based on code by E. Kriventseva
#
#orthologer is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at your option) any later version.
#
#orthologer is distributed in the hope that it will be useful,
#but WITHOUT ANY WARRANTY; without even the implied warranty of
#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License
#along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
set -u

# get pipeline dir
echo "DIR_ORTHOLOGER = $DIR_ORTHOLOGER"
echo "LOADED_COMMON_PIPELINE_SH = $LOADED_COMMON_PIPELINE_SH"

DIR_ORTHOLOGER=${DIR_ORTHOLOGER="$(cd -P "$(dirname "${BASH_SOURCE[0]}")"/../ && pwd)"}
[[ -f "${DIR_ORTHOLOGER}/bin/common_odb.sh" ]] || { echo "ERROR unable to read system common_odb.sh : $DIR_ORTHOLOGER/bin/common_odb.sh" 1>&2; exit 255; }
source "${DIR_ORTHOLOGER}/bin/common_odb.sh"

# just to avoid a warning
export DATA_TYPE=PROT

source ${DIR_ORTHOLOGER}/scheduler_common.sh
###setup_environment
op_step_setup
pl_dump_common_sh
