singularity-builds/htslib/htslib.def

Bootstrap: library
From: default/alpine:3.14.0

%post
  # Get the actual dependencies
  apk add --no-cache zlib bash libcurl

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

  # Make versioning easier
  HTSLIB_VERSION='1.13'

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

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

%test
  test_command () {
    if ! command -v "${1}"; then
      echo "command ${1} not found!"
      export FAILED_TESTS=1
    fi
  }

  test_command bash
  test_command ps

  if [ -n "$FAILED_TESTS" ]; then
    exit 1
  fi

%labels
  Author 25492070+MillironX@users.noreply.github.com
  SoftwareVersion 1.13
  SingularityDefinitionVersion 2

%help
  HTSlib
  ======

  HTSlib is an implementation of a unified C library for accessing common file
  formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data,
  and is the core library used by samtools and bcftools.

  For more help, see
  - <https://www.htslib.org>
  - <https://github.com/MillironX/singularity-builds>