mmseqs2: new package (#34189)

var/spack/repos/builtin/packages/mmseqs2/package.py

@@ -0,0 +1,39 @@
+# Copyright 2013-2022 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"
+
+    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")
+
+    # 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