From fcacf8dc9d6a989b61047f25441386b7811f65dc Mon Sep 17 00:00:00 2001 From: Justin S <3630356+codeandkey@users.noreply.github.com> Date: Wed, 27 May 2020 02:20:27 -0500 Subject: plink-ng: new package at v200511 (#16750) Co-authored-by: Massimiliano Culpo --- .../repos/builtin/packages/plink-ng/package.py | 38 ++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 var/spack/repos/builtin/packages/plink-ng/package.py 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) -- cgit v1.2.3-60-g2f50