#!/bin/bash

## Runs one stage of 04.3-methylKit-slurm.R in the Roberts Lab R container.
## Submit with 04.3-methylKit-slurm-submit.sh, which sets account, partition, resources, and working directory.

#SBATCH --job-name=04.3-methylKit
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=50G
#SBATCH --time=12:00:00

set -euo pipefail

# Same container and R library as the RStudio session used for 04.2
export APPTAINERENV_R_LIBS_USER=/mmfs1/gscratch/srlab/sr320/R_libs_apptainer
export APPTAINERENV_HI_PERC="${HI_PERC:-99.9}"

apptainer exec \
--home "$HOME" \
--bind /mmfs1/home/ \
--bind /mmfs1/gscratch/ \
--bind /gscratch/ \
/gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-46b5d9e.sif \
Rscript "${CODE_DIR}/04.3-methylKit-slurm.R" "$@"