—

if test -e /usr/local/parabricks/binaries/bin/collectmultiplemetrics ; then python3 -m pip install matplotlib ; fi

if test -e /usr/local/parabricks/TiedHash.pm ; then mv /usr/local/parabricks/TiedHash.pm /etc/perl/ ; fi

parabricks/ /usr/local/parabricks/

—

CUFILE_LOGFILE_PATH=/tmp/cufile.log

PATH=/usr/local/parabricks:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

APT_CUDA_VERSION=-12-2 apt update &&
  apt update --fix-missing &&
  apt -y upgrade

APT_CUDA_VERSION=-12-2 DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y bcftools python3 python3-distlib python3-pip zlib1g libboost-filesystem1.71.0 libboost-program-options1.71.0 libboost-iostreams1.71.0 libboost-system1.71.0 libbz2-1.0 libtcmalloc-minimal4 libisal2 libcufile-dev$APT_CUDA_VERSION gds-tools$APT_CUDA_VERSION samtools liblzma5 python3 perl libgomp1

APT_CUDA_VERSION=-12-2 apt update &&
  apt update --fix-missing