marcc-hpc/shortbred:latest

$ singularity pull shub://marcc-hpc/shortbred:latest

Singularity Recipe

Bootstrap: docker
From: biobakery/shortbred:latest

%environment
  # use bash as default shell
  SHELL=/bin/bash
  export SHELL

%setup
  # runs on host - the path to the image is $SINGULARITY_ROOTFS

%post
  # post-setup script

  # load environment variables
  . /environment

  # use bash as default shell and prepend /scratch/bin to PATH
  echo 'SHELL=/bin/bash' >> /environment
  echo 'PATH=/scratch/bin:$PATH' >> /environment
  echo 'export PATH' >> /environment
  echo '. /home/linuxbrew/.profile' >> /environment
  # make environment file executable
  chmod +x /environment

  # default mount paths
  mkdir /scratch /data 

%apprun identify
  exec shortbred_identify.py "$@"
  
%apprun quantify
  exec shortbred_quantify.py "$@" 
  
%test
  # test that script is a success

Collection

• Name: marcc-hpc/shortbred
• License: None

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