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!/bin/bash
###################################################################################################################################
#
# Copyright 2024 IRD
#
# This program 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.
#
# This program 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/> or
# write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston,
# MA 02110-1301, USA.
#
# Intellectual property belongs to IRD
# Version 1 and latter written by Francois Sabot
####################################################################################################################################
# Name will be setup at launch
#SBATCH --export=ALL
#SBATCH --mail-user francois.sabot@ird.fr
#SBATCH --mail-type=ALL
#SBATCH -p gpu
#SBATCH -c 24
#SBATCH -J LOchain
#SBATCH -nodelist=node7
#Data recovery
ANNOTATION = $1
SEQFOLDER = $2
OUTPUT = $3
#Modules used
module load liftoff/1.6.3
#Standard command for liftoff: "liftoff [-h] (-g GFF | -db DB) [-o FILE] [-u FILE] [-exclude_partial] [-dir DIR] [-mm2_options =STR] [-a A] [-s S] [-d D] [-flank F] [-V] [-p P] [-m PATH] [-f TYPES] [-infer_genes] [-infer_transcripts]
# [-chroms TXT] [-unplaced TXT] [-copies] [-sc SC] [-overlap O] [-mismatch M] [-gap_open GO] [-gap_extend GE] [-polish] [-cds]
# target reference""