Bootstrap: library
From: default/alpine:3.14.0

%post
  # Part 1: Install Samtools
  # ========================

  # Get the actual dependencies
  apk add --no-cache ncurses libbz2 xz zlib

  # Get the build dependencies
  apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev

  # Make versioning easier
  SAMTOOLS_VERSION='1.13'

  # Download the source tarball and build
  cd /tmp || exit 1
  wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
  tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
  cd samtools-$SAMTOOLS_VERSION || exit 1
  ./configure
  make && make install
  cd .. || exit 1
  rm -rf samtools-$SAMTOOLS_VERSION*
  cd || exit 1

  # Cleanup build packages
  apk del --no-cache .build-deps

  # Part 2: Install VarScan
  # ========================

  # Install java
  apk add --no-cache openjdk8

  # Make versioning easier
  VARSCAN_VERSION='v2.4.4'

  # Download varscan
  wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar -O /opt/varscan.jar

  # Create a shim for varscan
  echo "#!/bin/bash" > /usr/local/bin/varscan
  echo "java -jar /opt/varscan.jar \"\$@\"" >> /usr/local/bin/varscan
  chmod +x /usr/local/bin/varscan

  # Part 3: Install Nextflow dependencies
  # =====================================
  apk add --no-cache bash

%test
  cat << "EOF" > /tmp/singularity-test.sh
  #!/bin/bash
  CMDS=('bash' 'ps' 'java' 'varscan' 'samtools')
  for CMD in "${CMDS[@]}"; do
    if ! command -v "$CMD"; then
      echo "command $CMD not found!"
      FAILED_TESTS=1
    fi
  done
  # Abort if a test failed
  if [ -n "$FAILED_TESTS" ]; then
    exit 1
  fi
  EOF
  chmod +x /tmp/singularity-test.sh
  bash /tmp/singularity-test.sh

%runscript
  varscan "$@"

%labels
  Author 25492070+MillironX@users.noreply.github.com
  SoftwareVersion v2.4.4
  SingularityDefinitionVersion 2

%help
  VarScan
  =======

  VarScan is a platform-independent mutation caller for targeted, exome, and
  whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM,
  Roche/454, and similar instruments. It can be used to detect different types
  of variation:
  - Germline variants (SNPs an dindels) in individual samples or pools of samples.
  - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
  - Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
  - Somatic copy number alterations (CNAs) in tumor-normal exome data.

  For more help, see
  - <https://dkoboldt.github.io/varscan/>
  - <https://github.com/MillironX/singularity-builds>