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# Copyright 2013-2024 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.package import *
class Glfmultiples(MakefilePackage):
"""glfMultiples is a GLF-based variant caller for next-generation
sequencing data. It takes a set of GLF format genotype likelihood
files as input and generates a VCF-format set of variant calls
as output."""
homepage = "https://genome.sph.umich.edu/wiki/GlfMultiples"
url = "http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz"
license("BSD-3-Clause")
version(
"2010-06-16", sha256="f7abef6f6b043e9052fb408bb2aae6d0d97d907aedc1b3e02dd0db08eb81b979"
)
depends_on("zlib-api")
def edit(self, spec, prefix):
makefile = FileFilter("Makefile")
makefile.filter("CXX=.*", "CXX = " + env["CXX"])
makefile.filter(
"CFLAGS=.*",
"CFLAGS=-O2 -I./libsrc -I./pdf " + "-D_FILE_OFFSET_BITS=64 -D__USE_LONG_INT",
)
def install(self, spec, prefix):
make("INSTALLDIR=%s" % prefix, "install")
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