—

apt update &&
  apt update --fix-missing &&
  apt -y upgrade

/bin/bash -c apt-get update; apt-get install -y --no-install-recommends ./debian_package/artifact_folder_core/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_bam2fq/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_mutectcaller/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_collectmultiplemetrics/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_bqsr/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_bammetrics/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_genotypegvcf/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_dbsnp/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_starfusion/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_postpon/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_prepon/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_indexgvcf/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_applybqsr/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_fq2bam/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_rna-fq2bam/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_haplotypecaller/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_bamsort/*.deb &&
  apt-get install -y --no-install-recommends ./debian_package/artifact_folder_deepvariant/*.deb; dpkg -l | grep parabricks; apt-get install -y --no-install-recommends python3-pip; python3 -m pip install matplotlib;

NVIDIA_DRIVER_CAPABILITIES=compute,utility

NVIDIA_VISIBLE_DEVICES=all

NGC-DL-CONTAINER-LICENSE /

LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64

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

TARGETARCH=amd64 echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf &&
  echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf

TARGETARCH=amd64 apt-get update &&
  apt-get install -y --no-install-recommends cuda-cudart-11-2=${NV_CUDA_CUDART_VERSION} ${NV_CUDA_COMPAT_PACKAGE} &&
  ln -s cuda-11.2 /usr/local/cuda &&
  rm -rf /var/lib/apt/lists/*