spack/var/spack/repos/builtin/packages/shapeit4/package.py
Todd Gamblin a8ccb8e116 copyrights: update all files with license headers for 2021
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
      `spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
      for oneapi.py
2021-01-02 12:12:00 -08:00

56 lines
1.9 KiB
Python

# 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 Shapeit4(MakefilePackage):
"""SHAPEIT4 is a fast and accurate method for estimation of haplotypes
(aka phasing) for SNP array and high coverage sequencing data."""
homepage = "https://odelaneau.github.io/shapeit4/"
url = "https://github.com/odelaneau/shapeit4/archive/v4.1.3.tar.gz"
version('4.1.3', sha256='d209731277b00bca1e3478b7e0a0cbe40fbe23826c3d640ad12e0dd6033cbbb8')
maintainers = ['ilbiondo']
depends_on('htslib')
depends_on('boost')
depends_on('bzip2')
depends_on('xz')
def edit(self, spec, prefix):
makefile = FileFilter('makefile')
makefile.filter('CXX=.*', 'CXX = c++')
makefile.filter('CXXFLAG=.*', 'CXXFLAG = -O3')
makefile.filter('LDFLAG=.*', 'LDFLAG = -O3')
makefile.filter('HTSLIB_INC=.*', 'HTSLIB_INC = '
+ self.spec['htslib'].prefix.include)
makefile.filter('HTSLIB_LIB=.*', 'HTSLIB_LIB = '
+ self.spec['htslib'].prefix.lib + '/libhts.so')
makefile.filter('BOOST_INC=.*', 'BOOST_INC = '
+ self.spec['boost'].prefix.include)
makefile.filter('BOOST_LIB_IO=.*', 'BOOST_LIB_IO = '
+ self.spec['boost'].prefix.lib
+ "/libboost_iostreams.so")
makefile.filter('BOOST_LIB_PO=.*', 'BOOST_LIB_PO = '
+ self.spec['boost'].prefix.lib
+ "/libboost_program_options.so")
def install(self, spec, prefix):
install_tree('bin', prefix.bin)
install_tree('test', join_path(self.prefix, 'test'))
install_tree('docs', join_path(self.prefix, 'docs'))
install_tree('maps', join_path(self.prefix, 'maps'))