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# Copyright 2013-2023 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.package 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,
)
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