powerPlant/checkm-srf:1.0.13

$ singularity pull shub://powerPlant/checkm-srf:1.0.13

Singularity Recipe

# This recipe has been adapted from https://github.com/virus-x-eu/tools/blob/master/checkm/1.0.12/Dockerfile. Thank you @maitai.

Bootstrap: docker
From: ubuntu:bionic

%labels
Maintainer eric.burgueno@plantandfood.co.nz
Version 1.0.13

%post
  ## Download build prerequisites
  apt-get update
  apt-get -y install hmmer prodigal python python-pip unzip wget

  ## Download dependencies
  wget https://github.com/matsen/pplacer/releases/download/v1.1.alpha19/pplacer-linux-v1.1.alpha19.zip
  unzip pplacer-linux-v1.1.alpha19.zip
  cp -r pplacer-Linux-v1.1.alpha19/* /usr/local/bin/

  ## Install checkm
  pip install checkm-genome==1.0.13

  ## Configure data location (must be bind-mounted)
  echo '{"dataRoot": "/media", "remoteManifestURL": "https://data.ace.uq.edu.au/public/CheckM_databases/", "manifestType": "CheckM", "remoteManifestName": ".dmanifest", "localManifestName": ".dmanifest"}' > /usr/local/lib/python2.7/dist-packages/checkm/DATA_CONFIG

  ## Cleanup
  rm -rf pplacer*
  apt-get -y remove unzip wget
  apt-get -y autoremove
  apt-get -y clean all

%runscript
  if [ ! -f /media/.dmanifest ]; then
    exec /bin/echo -e "This container requires that you bind mount the location to CheckM data into /media. Please use \"singularity run -B <path_to_checkm_data>:/media $SINGULARITY_NAME\" and try again. You can download the latest version of the CheckM data files from https://data.ace.uq.edu.au/public/CheckM_databases/. See https://github.com/Ecogenomics/CheckM/wiki/Installation#how-to-install-checkm for more information."
  else
    exec checkm "$@"
  fi

Collection

• Name: powerPlant/checkm-srf
• License: None

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