Tips collected in an template

Ubuntu definition file

Bootstrap: docker
From: ubuntu:22.04

%environment
  export LC_ALL=C
  export PYTHONNOUSERSITE=True

%post
  export LC_ALL=C
  export PYTHONNOUSERSITE=True
  export DEBIAN_FRONTEND=noninteractive

  # apt packages cached in /tmp
  mkdir -p /tmp/apt22 &&  echo "Dir::Cache "/tmp/apt22";" > /etc/apt/apt.conf.d/singularity-cache.conf

  apt-get update && apt-get -y dist-upgrade && \
  apt-get install -y


  # Download
  # export TMPD=/tmp/downloads &&   mkdir -p $TMPD
  # wget -P $TMPD -c  ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz
  # gunzip -c $TMPD/human_g1k_v37.fasta.gz > human_g1k_v37.fasta || true


  # pip cache in /tmp
  # export PIP_TMP=/tmp/pip-cache ;  mkdir -p $PIP_TMP
  # python3 -m pip install --cache-dir $PIP_TMP --upgrade pip setuptools wheel

  # pip without caching
  # python3 -m pip install --no-cache-dir       --upgrade pip setuptools wheel


  # Sourcing file when running/executing the container
  # cp /usr/local/gromacs/bin/ACTRC.bash   /.singularity.d/env/99-ACTRC.sh

# cat to a file
#cat << EOF > /tmp/myfile
#EOF

  # Patch for old kernels
  # strip --remove-section=.note.ABI-tag /usr/lib/x86_64-linux-gnu/libQt5Core.so.5 

%runscript
#!/bin/sh
  if command -v $SINGULARITY_NAME > /dev/null 2> /dev/null; then
    exec $SINGULARITY_NAME "$@"
  else
    echo "# ERROR !!! Command $SINGULARITY_NAME not found in the container"
  fi