cottersci/DIRT2_Workflows:dirt2d

$ singularity pull shub://cottersci/DIRT2_Workflows:dirt2d

Singularity Recipe

Bootstrap: shub
From: Computational-Plant-Science/DIRT

%labels
  Maintainer Chris Cotter (cotter@uga.edu)
  Version v0.0

%setup
  mkdir -p ${SINGULARITY_ROOTFS}/workflow

%files
  dirt2D.nf /workflow/

%post
  #By default, nextflow writes cache and framework files to ~/.nextflow.
  # this variable is set to move that
  export NXF_HOME="/opt/.nextflow"

  apt-get update
  apt-get -y install openjdk-8-jre-headless wget

  cd /bin
  wget -qO- https://get.nextflow.io | bash
  chmod a+rx nextflow
  ./nextflow #Run nextflow to download and install remaining dependencies.
  chmod -R a+rwx $NXF_HOME

  apt-get -y install python3 python3-pip
  pip3 install git+https://github.com/cottersci/dirtweb_api.git#egg=dirtweb_api

  #cleanup
  apt-get purge
  apt-get clean

%environment
  export NXF_HOME="/opt/.nextflow"

%runscript
  /bin/nextflow run /workflow/dirt2D.nf  "$@"

Collection

• Name: cottersci/DIRT2_Workflows
• License: None

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