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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 Mmseqs2(CMakePackage):
"""MMseqs2 (Many-against-Many sequence searching) is a software suite to
search and cluster huge protein and nucleotide sequence sets"""
homepage = "https://github.com/soedinglab/MMseqs2"
url = "https://github.com/soedinglab/MMseqs2/archive/refs/tags/14-7e284.tar.gz"
license("GPL-3.0-only")
version("14-7e284", sha256="a15fd59b121073fdcc8b259fc703e5ce4c671d2c56eb5c027749f4bd4c28dfe1")
version("13-45111", sha256="6444bb682ebf5ced54b2eda7a301fa3e933c2a28b7661f96ef5bdab1d53695a2")
variant("openmp", default=False, description="build with OpenMP support")
variant("mpi", default=False, description="build with MPI support")
depends_on("zstd")
depends_on("mpi", when="+mpi")
# patch to support building with gcc@13:
patch(
"https://github.com/soedinglab/MMseqs2/commit/3e43617.patch?full_index=1",
sha256="673737ac545260e7800ca191c6eee14feef3318d9cfa5005db32bd2ab3c006fe",
when="%gcc@13:",
level=1,
)
# apple-clang will build with +openmp with llvm-openmp as a dependency
# however when running with real data, it threw segmentation faults
conflicts("%apple-clang", when="+openmp")
def cmake_args(self):
spec = self.spec
args = []
args.append("-DVERSION_OVERRIDE=%s" % self.spec.version)
args.append("-DUSE_SYSTEM_ZSTD=1")
if "~openmp" in spec:
args.append("-DREQUIRE_OPENMP=0")
if "~mpi" in spec:
args.append("-DHAVE_MPI=0")
return args
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