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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)
import numbers
from spack.package import *
from spack.pkg.builtin.boost import Boost
def is_multiple_32(x):
"""multiple of 32"""
try:
return (
isinstance(int(x), numbers.Integral) and not isinstance(x, bool) and int(x) % 32 == 0
)
except ValueError:
return False
class Abyss(AutotoolsPackage):
"""ABySS is a de novo, parallel, paired-end sequence assembler
that is designed for short reads. The single-processor version
is useful for assembling genomes up to 100 Mbases in size."""
homepage = "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
url = "https://github.com/bcgsc/abyss/releases/download/2.3.1/abyss-2.3.1.tar.gz"
version("2.3.5", sha256="5455f7708531681ee15ec4fd5620526a53c86d28f959e630dc495f526b7d40f7")
version("2.3.1", sha256="664045e7903e9732411effc38edb9ebb1a0c1b7636c64b3a14a681f465f43677")
version("2.3.0", sha256="3df923b0699187fb27948cae43293eeb5745161d5dc484b9befbe2ca8efb6ad7")
version("2.2.5", sha256="38e886f455074c76b32dd549e94cc345f46cb1d33ab11ad3e8e1f5214fc65521")
version("2.1.4", sha256="2145a1727556104d6a14db06a9c06f47b96c31cc5ac595ae9c92224349bdbcfc")
version("2.0.2", sha256="d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df")
version("1.5.2", sha256="8a52387f963afb7b63db4c9b81c053ed83956ea0a3981edcad554a895adf84b1")
variant(
"maxk", default=128, values=is_multiple_32, description="set the maximum k-mer length."
)
depends_on("autoconf", type="build")
depends_on("automake", type="build")
depends_on("bwa", type="run")
depends_on("mpi")
depends_on("boost@:1.50.0,1.53.0:", when="@2.0.2:")
depends_on("boost@:1.50.0,1.53.0:1.59.0", when="@:1.5.2")
# Maintainers: Is boost really a dependency? In what conditions?
depends_on(Boost.with_default_variants)
depends_on("sparsehash")
depends_on("sqlite")
depends_on("libtool")
conflicts("^intel-mpi")
conflicts("^intel-parallel-studio+mpi")
conflicts("^mvapich2")
conflicts("^spectrum-mpi")
def configure_args(self):
maxk = int(self.spec.variants["maxk"].value)
args = [
f"--with-boost={self.spec['boost'].prefix}",
f"--with-sqlite={self.spec['sqlite'].prefix}",
f"--with-mpi={self.spec['mpi'].prefix}",
]
if maxk:
args.append(f"--enable-maxk={maxk}")
if self.spec["mpi"].name == "mpich":
args.append("--enable-mpich")
return args
patch("fix_BloomFilter.hpp.patch", when="@2.0.0:2.1.4")
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