singularity.def

Bootstrap: docker
From: python:3.11-slim

%files
  . /opt/occufold_src

%post
  set -eux
  apt-get update && apt-get install -y --no-install-recommends \
      build-essential git ca-certificates procps && \
      rm -rf /var/lib/apt/lists/*

  python -m pip install --upgrade pip setuptools wheel

  # Pick the requirements file; install your deps
  REQ=/opt/occufold_src/requirements.txt
  [ -f "$REQ" ] || REQ=/opt/occufold_src/OccuFold/requirements.txt || true
  if [ -f "$REQ" ]; then
    python -m pip install --no-cache-dir --prefix=/usr/local -r "$REQ"
  else
    python -m pip install --no-cache-dir --prefix=/usr/local \
      "numpy>=1.26" "pandas>=2.0" "bioframe>=0.4" "cooler>=0.9" "pysam>=0.22" "torch>=2.2,<3" "cooltools>=0.6.1"
  fi

  # Ensure plotting + cooltools stack (prefer wheels; pin numba for py3.11)
  python -m pip install --no-cache-dir --prefix=/usr/local --only-binary=:all: \
    "scipy>=1.10" "numba<0.60" "matplotlib>=3.8" "h5py>=3.10" "networkx>=3.2" \
    "cooltools>=0.6.1" "pyBigWig>=0.3.22"

  # If torch didn’t come from PyPI (some sites don’t host CPU wheels), fetch from PyTorch’s CPU index
  python - <<'PY' || true
import importlib; import sys
sys.exit(0 if importlib.util.find_spec("torch") else 1)
PY
  [ $? -eq 0 ] || python -m pip install --no-cache-dir --prefix=/usr/local --index-url https://download.pytorch.org/whl/cpu torch

# Sanity-check key imports; fail fast if any are missing
python - <<'PY'
import numpy, pandas, pysam, torch, cooltools, pyBigWig 
print("PYBIGWIG_OK", pyBigWig.__version__)
print("NUMPY_OK", numpy.__version__)
print("PANDAS_OK", pandas.__version__)
print("PYSAM_OK", pysam.__version__)
print("TORCH_OK", torch.__version__, "CUDA:", torch.cuda.is_available())
print("COOLTOOLS_OK", cooltools.__version__)
PY

  # Quiet Singularity bind warnings
  mkdir -p /tmp /var/tmp /proc /etc
  : > /etc/passwd; : > /etc/group; : > /etc/hosts; : > /etc/resolv.conf

%environment
  # Keep your dev-mode import path
  export PYTHONPATH=/opt/occufold_src
  export PATH=/opt/occufold_src/scripts:$PATH

%runscript
  exec "$@"