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# 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)
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