d0589285f7
* unmaintained pkgs: bump versions 2024-05-10 * openblas: fix satisfies syntax * pixman: add autotools dependencies * [@spackbot] updating style on behalf of alecbcs * pixman: revert * chapel: revert changes in favor of other PR * openblas: revert due to failing tests * Address review feedback for flint, biobam2, and pango * pango: add version comment about v2.0 * numactl: revert changes due to ppc4le bug * flint: remote duplicate configure arg Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> * openvkl, rkcommon: remove commented maintainers template * flint: fix style --------- Co-authored-by: alecbcs <alecbcs@users.noreply.github.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
46 lines
1.8 KiB
Python
46 lines
1.8 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Biobambam2(AutotoolsPackage):
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"""Tools for early stage alignment file processing"""
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homepage = "https://gitlab.com/german.tischler/biobambam2"
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url = "https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz"
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version(
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"2.0.177",
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sha256="ad0a418fb49a31996a105a1a275c0d1dfc8b84aa91d48fa1efb6ff4fe1e74181",
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url="https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.177-release-20201112105453/biobambam2-2.0.177-release-20201112105453.tar.gz",
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)
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depends_on("autoconf", type="build")
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depends_on("automake", type="build")
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depends_on("libtool", type="build")
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depends_on("m4", type="build")
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depends_on("libmaus2")
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test_src_dir = "test"
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def configure_args(self):
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args = [f"--with-libmaus2={self.spec['libmaus2'].prefix}"]
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return args
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@run_after("install")
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def cache_test_sources(self):
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"""Copy the test source files after the package is installed to an
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install test subdirectory for use during `spack test run`."""
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self.cache_extra_test_sources(self.test_src_dir)
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def test_short_sort(self):
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"""run testshortsort.sh to check alignments sorted by coordinate"""
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test_dir = join_path(self.test_suite.current_test_cache_dir, self.test_src_dir)
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with working_dir(test_dir):
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sh = which("sh")
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out = sh("testshortsort.sh", output=str.split, error=str.split)
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assert "Alignments sorted by coordinate." in out
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