plink-ng: new package at v200511 (#16750)

Co-authored-by: Massimiliano Culpo <massimiliano.culpo@gmail.com>

1 files changed, 38 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/plink-ng/package.py b/var/spack/repos/builtin/packages/plink-ng/package.py
new file mode 100644
index 0000000000..27b4a4ca95
--- /dev/null
+++ b/var/spack/repos/builtin/packages/plink-ng/package.py
@@ -0,0 +1,38 @@
+# Copyright 2013-2020 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 import *
+
+
+class PlinkNg(Package):
+    """A comprehensive update to the PLINK association analysis toolset."""
+
+    homepage = "https://www.cog-genomics.org/plink/2.0/"
+    url      = "https://www.cog-genomics.org/static/bin/plink2_src_200511.zip"
+
+    version('200511', sha256='00cff19bece88acb7a21ba098501cb677b78d22c9f3ca5bcdc869139a40db816')
+
+    depends_on('zlib')
+    depends_on('zstd@1.4.4:')
+    depends_on('cblas')
+    depends_on('blas')
+    depends_on('lapack')
+
+    conflicts('%gcc@:4.99')
+
+    def url_for_version(self, ver):
+        template = 'https://www.cog-genomics.org/static/bin/plink2_src_{0}.zip'
+        return template.format(ver)
+
+    def setup_build_environment(self, env):
+        zlib = join_path(self.spec['zlib'].prefix.lib, 'libz.a')
+        env.set('ZLIB', zlib)
+
+    def install(self, spec, prefix):
+        ld_flags = [spec['lapack'].libs.ld_flags, spec['blas'].libs.ld_flags]
+        filter_file('-llapack -lcblas -lblas', ' '.join(ld_flags),
+                    'build.sh', string=True)
+        which('sh')('build.sh')
+        install_tree('.', prefix)