#!/bin/bash

## Runs one stage of 04.6-methylKit-DMR-slurm.R in the Roberts Lab R container.
## Submit with 04.6-methylKit-DMR-slurm-submit.sh, which sets account, partition, resources, and working directory.
## R packages come from the same R library as 04.3 (methylKit 1.32.1)

#SBATCH --job-name=04.6-methylKit-DMR
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=16G
#SBATCH --time=12:00:00

set -euo pipefail

export APPTAINERENV_R_LIBS_USER=/mmfs1/gscratch/srlab/sr320/R_libs_apptainer

# Settings read by 04.6-methylKit-DMR-slurm.R
for v in HI_PERC REGIONS COV_BASES LO_COUNT SAMPLES OVERDISPERSION PERM PERM_SCHEME; do
  [ -n "${!v:-}" ] && export "APPTAINERENV_${v}=${!v}"
done

apptainer exec \
--home "$HOME" \
--bind /mmfs1/home/ \
--bind /mmfs1/gscratch/ \
--bind /gscratch/ \
/gscratch/srlab/containers/srlab-R4.4-bioinformatics-container-46b5d9e.sif \
Rscript "${R_SCRIPT:-${CODE_DIR}/04.6-methylKit-DMR-slurm.R}" "$@" #R_SCRIPT: copy made at submission (see the submit script)