path: root/var/spack/repos/builtin/packages/admixtools/package.py

# 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 import *


class Admixtools(MakefilePackage):
    """The ADMIXTOOLS package implements 5 methods described in
    Patterson et al. (2012) Ancient Admixture in Human History. Details
    of the methods and algorithm can be found in this paper.."""

    homepage = "https://github.com/DReichLab/AdmixTools"
    url      = "https://github.com/DReichLab/AdmixTools/archive/v7.0.2.tar.gz"

    version('7.0.2', sha256='d1dc1963e01017f40e05e28009008e14388a14a3facc75cff46653da585bd91e')
    version('7.0.1', sha256='182dd6f55109e9a1569b47843b0d1aa89fe4cf4a05f9292519b9811faea67a20')
    version('7.0', sha256='c00faab626f02bbf9c25c6d2dcf661db225776e9ed61251f164e5edeb5a448e5')
    version('6.0', sha256='8fcd6c6834c7b33afdd7188516856d9c66b53c33dc82e133b72b56714fb67ad5')
    version('5.1', sha256='42b584cc785abfdfa9f39a341bdf81f800639737feaf3d07702de4a2e373557e')
    version('5.0', sha256='9f00637eac84c1ca152b65313d803616ee62c4156c7c737a33f5b31aeeac1367')
    version('1.0.1', sha256='ef3afff161e6a24c0857678373138edb1251c24d7b5308a07f10bdb0dedd44d0')
    version('1.0', sha256='cf0d6950285e801e8a99c2a0b3dbbbc941a78e867af1767b1d002ec3f5803c4b')

    depends_on('lapack')
    depends_on('gsl')

    build_directory = 'src'

    def edit(self, spec, prefix):
        makefile = FileFilter('src/Makefile')

        lapackflags = spec['lapack'].libs.ld_flags

        makefile.filter('override LDLIBS += -lgsl -lopenblas -lm -lnick',
                        'override LDLIBS += -lgsl -lm -lnick ' + lapackflags)

        makefile.filter('TOP=../bin', 'TOP=./bin')

    def install(self, spec, prefix):
        with working_dir('src'):

            make('install')
            install_tree('bin', prefix.bin)
            install('twtable', prefix.bin)