old_contents: # Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  
  
  class Biobambam2(AutotoolsPackage):
      """Tools for early stage alignment file processing"""
  
      homepage = "https://gitlab.com/german.tischler/biobambam2"
      url      = "https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz"
  
      version('2.0.177', sha256='ad0a418fb49a31996a105a1a275c0d1dfc8b84aa91d48fa1efb6ff4fe1e74181',
              url='https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
      depends_on('libmaus2')
  
      test_src_dir = 'test'
  
      def configure_args(self):
          args = ['--with-libmaus2={0}'.format(self.spec['libmaus2'].prefix)]
          return args
  
      def _fix_shortsort(self):
          """Fix the testshortsort.sh file copied during installation."""
          test_dir = join_path(self.install_test_root, self.test_src_dir)
          filter_file('../src/', '', join_path(test_dir, 'testshortsort.sh'))
  
      @run_after('install')
      def cache_test_sources(self):
          """Copy the test source files after the package is installed to an
          install test subdirectory for use during `spack test run`."""
          self.cache_extra_test_sources(self.test_src_dir)
          self._fix_shortsort()
  
      def test(self):
          test_dir = join_path(self.install_test_root, self.test_src_dir)
          self.run_test('sh', ['testshortsort.sh'],
                        expected='Alignments sorted by coordinate.',
                        work_dir=test_dir)
  
new_contents: # Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
  # Spack Project Developers. See the top-level COPYRIGHT file for details.
  #
  # SPDX-License-Identifier: (Apache-2.0 OR MIT)
  
  from spack import *
  
  
  class Biobambam2(AutotoolsPackage):
      """Tools for early stage alignment file processing"""
  
      homepage = "https://gitlab.com/german.tischler/biobambam2"
      url      = "https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz"
  
      version('2.0.177', sha256='ad0a418fb49a31996a105a1a275c0d1dfc8b84aa91d48fa1efb6ff4fe1e74181',
              url='https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz')
  
      depends_on('autoconf', type='build')
      depends_on('automake', type='build')
      depends_on('libtool',  type='build')
      depends_on('m4',       type='build')
      depends_on('libmaus2')
  
      test_src_dir = 'test'
  
      def configure_args(self):
          args = ['--with-libmaus2={0}'.format(self.spec['libmaus2'].prefix)]
          return args
  
      def _fix_shortsort(self):
          """Fix the testshortsort.sh file copied during installation."""
          test_dir = join_path(self.install_test_root, self.test_src_dir)
          filter_file('../src/', '', join_path(test_dir, 'testshortsort.sh'))
  
      @run_after('install')
      def cache_test_sources(self):
          """Copy the test source files after the package is installed to an
          install test subdirectory for use during `spack test run`."""
          self.cache_extra_test_sources(self.test_src_dir)
          self._fix_shortsort()
  
      def test(self):
          """Perform stand-alone/smoke test on installed package."""
          test_dir = join_path(self.test_suite.current_test_cache_dir,
                               self.test_src_dir)
          self.run_test('sh', ['testshortsort.sh'],
                        expected='Alignments sorted by coordinate.',
                        purpose='test: checking alignments',
                        work_dir=test_dir)
  
subject: update stand-alone tests to use test stage work directory (#24111)