p2e_singularity.def

Bootstrap: docker
From: rocker/tidyverse:4.1.1

%files
  .credentials
  helptext.sh

%post
  chmod 644 /.credentials
  apt-get update && apt-get install -y libmariadb-dev
  R --slave -e 'install.packages(c("remotes", "DBI", "RMariaDB", "optparse"))'
  R --slave -e 'remotes::install_github("sidora-tools/sidora.core", dependencies = TRUE)'
  R --slave -e 'remotes::install_github("sidora-tools/pandora2eager", dependencies = TRUE)'

%runscript
  #!/bin/bash
  export input=$1

  if [[ ${#@} == 0 || $1 == "-h" || $1 == "--help" ]]; then
    bash /helptext.sh
  elif [[ ${#@} -gt 1 ]]; then
    shift
    Rscript  --vanilla /usr/local/lib/R/site-library/pandora2eager/exec/pandora2eager.R ${input} /.credentials $*
  else
    Rscript  --vanilla /usr/local/lib/R/site-library/pandora2eager/exec/pandora2eager.R ${input} /.credentials
  fi

%labels
  Author  Thiseas C. Lamnidis
  GithubUrl https://github.com/sidora-tools/pandora2eager.git
  Version 0.6.0