powerPlant/novograph-srf:1.0.0

$ singularity pull shub://powerPlant/novograph-srf:1.0.0

Singularity Recipe

Bootstrap: docker
From: ubuntu:bionic

%labels
Maintainer eric.burgueno@plantandfood.co.nz
Version 1.0.0

%post
  ## Download prerequisites
  apt-get update
  apt-get -y install bioperl bwa g++ gcc git libbz2-dev liblzma-dev libmodule-build-perl libset-intervaltree-perl mafft make samtools sudo wget zlib1g-dev

  ## BIO::DB::HTS
  cd /opt
  wget https://github.com/Ensembl/Bio-DB-HTS/archive/2.11.tar.gz
  tar -xzf 2.11.tar.gz
  cd Bio-DB-HTS-2.11
  ./INSTALL.pl 

  ## NovoGraph
  cd /opt
  wget https://github.com/NCBI-Hackathons/NovoGraph/archive/v1.0.0.tar.gz
  tar -xzf v1.0.0.tar.gz 
  cd NovoGraph-1.0.0/src
  make all

  ## Cleanup
  SUDO_FORCE_REMOVE=yes apt-get -y remove g++ gcc git libbz2-dev liblzma-dev libmodule-build-perl make sudo wget zlib1g-dev
  apt-get -y autoremove
  apt-get -y clean all

%runscript
if [ $# -eq 0 ]; then
  /bin/echo -e "This Singularity image cannot provide a single entrypoint. Please use \"$SINGULARITY_NAME <cmd>\" or \"singularity exec $SINGULARITY_NAME perl <cmd>\", where <cmd> is one of the following:\n"
  exec ls /opt/NovoGraph-1.0.0/scripts
else
  cd /opt/NovoGraph-1.0.0/scripts
  exec perl "$@"
fi

Collection

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

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