plink2: add new package @2.00a4.3 (#38469)

Co-authored-by: LMS Bioinformatics <bioinformatics@lms.mrc.ac.uk>

1 files changed, 49 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/plink2/package.py b/var/spack/repos/builtin/packages/plink2/package.py
new file mode 100644
index 0000000000..7846f5ae4d
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plink2/package.py
@@ -0,0 +1,49 @@
+# 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 Plink2(MakefilePackage):
+    """PLINK2: Whole genome association analysis toolset, designed to perform a
+    range of basic, large-scale analyses in a computationally efficient manner."""
+
+    homepage = "https://www.cog-genomics.org/plink/2.0/"
+    git = "https://github.com/chrchang/plink-ng.git"
+
+    version("2.00a4.3", tag="v2.00a4.3")
+
+    depends_on("zlib@1.2.12:")
+    depends_on("zstd@1.5.2:")
+    depends_on("libdeflate@1.10:")
+    depends_on("blas")
+    depends_on("lapack")
+
+    build_directory = "2.0/build_dynamic"
+
+    def edit(self, spec, prefix):
+        with working_dir(self.build_directory):
+            makefile = FileFilter("Makefile")
+            if "avx2" in spec.target:
+                makefile.filter(r"^NO_AVX2 = 1", "NO_AVX2 =")
+            elif "sse4_2" in spec.target:
+                makefile.filter(r"^NO_SSE42 = 1", "NO_SSE42 =")
+            makefile.filter(r"^STATIC_ZSTD = 1", "STATIC_ZSTD =")
+            makefile.filter(
+                r"^  BLASFLAGS=-llapack -lblas -lcblas -latlas",
+                "  BLASFLAGS={0} {1}".format(
+                    spec["blas"].libs.ld_flags, spec["lapack"].libs.ld_flags
+                ),
+            )
+
+    def build(self, spec, prefix):
+        with working_dir(self.build_directory):
+            make()
+
+    def install(self, spec, prefix):
+        mkdir(prefix.bin)
+        with working_dir(self.build_directory):
+            install("plink2", prefix.bin)
+            install("pgen_compress", prefix.bin)