#!/bin/bash

## Runs one stage of 04.4-DSS-slurm.R in the Roberts Lab R container.
## Submit with 04.4-DSS-slurm-submit.sh, which sets account, partition, resources, and working directory.
## R packages come from R_LIBS_USER in ~/.Renviron (/mmfs1/home/sr320/R_libs_apptainer), which has DSS 2.54.0 and bsseq 1.42.0

#SBATCH --job-name=04.4-DSS
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=16G
#SBATCH --time=12:00:00

set -euo pipefail

# Settings read by 04.4-DSS-slurm.R
for v in LO_COV HI_PERC PRESENCE MIN_METH SNP_FILTER SAMPLES MODEL GENO_PCS PERM NCHUNK; 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:-${CODE_DIR}/04.4-DSS-slurm.R}" "$@"