From d1e01d5646b43bf3afbd04f2593f529f606426ad Mon Sep 17 00:00:00 2001 From: George Young Date: Tue, 13 Feb 2024 17:02:44 +0000 Subject: khmer: new package @2.1.1 (#42450) * khmer: new package @2.1.1 * rationalising patch * adding dep, modifying patch * Update var/spack/repos/builtin/packages/khmer/package.py Indeed! Co-authored-by: Adam J. Stewart * Update package.py --------- Co-authored-by: LMS Bioinformatics Co-authored-by: Adam J. Stewart --- var/spack/repos/builtin/packages/khmer/package.py | 32 +++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 var/spack/repos/builtin/packages/khmer/package.py diff --git a/var/spack/repos/builtin/packages/khmer/package.py b/var/spack/repos/builtin/packages/khmer/package.py new file mode 100644 index 0000000000..c93b4fbacd --- /dev/null +++ b/var/spack/repos/builtin/packages/khmer/package.py @@ -0,0 +1,32 @@ +# Copyright 2013-2024 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 Khmer(PythonPackage): + """khmer is a software library and toolkit for k-mer based analysis and transformation + of nucleotide sequence data""" + + homepage = "https://khmer.readthedocs.io/en/latest/" + pypi = "khmer/khmer-2.1.1.tar.gz" + + license("BSD-3-Clause", checked_by="A-N-Other") + + version("2.1.1", sha256="a709606910bb8679bd8525e9d2bf6d1421996272e343b54cc18090feb2fdbe24") + + # https://github.com/dib-lab/khmer/pull/1922 ... + conflicts("^python@3.12:") + + depends_on("py-setuptools@3.4.1:", type="build") + depends_on("py-pytest-runner@2", type="build") + depends_on("py-screed@1:", type=("build", "run")) + # abandoned `bz2file` dependency dropped in favour of the patch below + + depends_on("openmpi") + + def patch(self): + filter_file("bz2file", "bz2", join_path("khmer", "kfile.py")) + filter_file("'bz2file', ", "", "setup.py") -- cgit v1.2.3-70-g09d2