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# Copyright 2013-2021 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 Plink(Package):
"""PLINK is a free, open-source 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/1.9/"
version('1.9-beta6.10', sha256='f8438656996c55a5edd95c223cce96277de6efaab1b9b1d457bfee0c272058d8',
url='http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip')
version('1.9-beta5', sha256='e00ef16ac5abeb6b4c4d77846bd655fafc62669fbebf8cd2e941f07b3111907e',
url='https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz')
version('1.07', sha256='70c52ee47eed854293832639dbabb41c7c036db3a4881c136e6a71ecff4ac7f4',
url='http://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip',
preferred=True)
depends_on('atlas', when='@1.9-beta5')
depends_on('netlib-lapack', when='@1.9-beta5')
depends_on('atlas', when='@1.9-beta6.10')
depends_on('netlib-lapack', when='@1.9-beta6.10')
def install(self, spec, prefix):
mkdirp(prefix.bin)
if spec.version == Version('1.07'):
install('plink', prefix.bin)
install('gPLINK.jar', prefix.bin)
if spec.version == Version('1.9-beta5'):
with working_dir('1.9'):
first_compile = Executable('./plink_first_compile')
first_compile()
install('plink', prefix.bin)
if spec.version == Version('1.9-beta6.10'):
install('plink', prefix.bin)
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