runDocker.sh

#!/bin/bash
set -euo pipefail

# Run runChromap.sh inside the Docker container with proper mounts/env
USER_ID=$(id -u)
GROUP_ID=$(id -g)
IMAGE="biodepot/chromap:0.3.2"

# Defaults (can override by exporting before calling this script)
FASTQ_DIR_DEFAULT="/storage/ATAC-Seq"
OUT_DIR_DEFAULT="/storage/ATAC-Seq/output"
HELPER_DIR_DEFAULT="/home/lhhung/chrombpnet/chrombpnet/helpers"
INDEX_FILE_DEFAULT="/storage/scRNAseq_output/indices-110-44/chromap/index"
REF_FASTA_DEFAULT="/storage/scRNAseq_output/indices-110-44/chromap/genome.fa"
CHROM_SIZES_DEFAULT="/storage/scRNAseq_output/indices-110-44/chromap/chrNameLength.txt"
OUTPUT_BAM_DIR_DEFAULT="/mnt/pikachu/ATAC-Seq_bamoutput"

echo "Running container as user ${USER_ID}:${GROUP_ID} using image ${IMAGE}"

# Attach a TTY only if stdout is a terminal
TTY_FLAGS=""
if [ -t 1 ]; then
  TTY_FLAGS="-it"
fi

docker run --rm ${TTY_FLAGS} \
  -u "${USER_ID}:${GROUP_ID}" \
  -v /storage:/storage \
  -v /mnt/pikachu:/mnt/pikachu \
  -v /home/lhhung:/home/lhhung \
  -v "${PWD}":"${PWD}" \
  -w "${PWD}" \
  -e FASTQ_DIR="${FASTQ_DIR:-${FASTQ_DIR_DEFAULT}}" \
  -e OUT_DIR="${OUT_DIR:-${OUT_DIR_DEFAULT}}" \
  -e HELPER_DIR="${HELPER_DIR:-${HELPER_DIR_DEFAULT}}" \
  -e INDEX_FILE="${INDEX_FILE:-${INDEX_FILE_DEFAULT}}" \
  -e REF_FASTA="${REF_FASTA:-${REF_FASTA_DEFAULT}}" \
  -e CHROM_SIZES="${CHROM_SIZES:-${CHROM_SIZES_DEFAULT}}" \
  -e OUTPUT_BAM_DIR="${OUTPUT_BAM_DIR:-${OUTPUT_BAM_DIR_DEFAULT}}" \
  -e TMPDIR="${OUT_DIR:-${OUT_DIR_DEFAULT}}/tmp" \
  -e MPLCONFIGDIR="/tmp/mpl" \
  -e PYTHONPATH="/home/lhhung/chrombpnet:${PYTHONPATH:-}" \
  -e THREADS="${THREADS:-16}" \
  -e JOBS="${JOBS:-1}" \
  -e DRYRUN="${DRYRUN:-0}" \
  "${IMAGE}" \
  bash -lc "mkdir -p \"\${TMPDIR}\" && cd \"\${TMPDIR}\" && ${PWD}/runChromap.sh $*"