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# Copyright 2013-2023 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 Hicops(CMakePackage):
"""HiCOPS is a software framework for accelerating database peptide search
workflows on supercomputers. HiCOPS provided algorithm-independent
parallelizations and optimizations can be extended into new HPC database search
algorithms or scalably accelerate the existing ones.
"""
homepage = "https://hicops.github.io/index"
git = "https://github.com/hicops/hicops.git"
maintainers("pcdslab", "mhaseeb123", "nessiecancode")
version("release", branch="release")
version("develop", branch="develop")
# Build Options
variant("mpi", default=True, description="Enable MPI support.")
variant(
"timemory",
default=False,
description="Enable timemory interface. Requires timemory " "installation.",
)
variant(
"mpip",
default=False,
description="Enables the MPIP data_tracker via Timemory. "
"Requires timemory installation.",
)
variant(
"tailfit",
default=True,
description="Use the tailfit method instead of Gumbelfit " "for e-value computation.",
)
variant("progress", default=True, description="Display HiCOPS progress marks.")
variant(
"seqlen",
default="60",
description="Allowed maximum peptide sequence length.",
values=int,
multi=False,
)
variant(
"qalen",
default="100",
description="Maximum number of top K peaks to keep when " "spectrum preprocess.",
values=int,
multi=False,
)
variant(
"qchunk",
default="10000",
description="Max size of each batch extracted from the " "dataset.",
values=int,
multi=False,
)
variant(
"hyperscore",
default="100",
description="Maximum allowed hyperscore computed.",
values=int,
multi=False,
)
variant(
"shdpeaks",
default="80",
description="Maximum shared b- or y-ions allowed.",
values=int,
multi=False,
)
variant("cxx_std", default="14", description="C++ standard", values=("14", "17"), multi=False)
depends_on("py-numpy")
depends_on("py-python-dateutil")
depends_on("py-setuptools")
depends_on("py-bottleneck")
depends_on("py-pyparsing")
depends_on("py-six")
depends_on("py-setuptools-scm")
depends_on("py-et-xmlfile")
depends_on("py-cython")
depends_on("py-cycler")
depends_on("py-pytz")
depends_on("py-kiwisolver")
depends_on("py-numexpr")
depends_on("py-matplotlib")
depends_on("py-jdcal")
depends_on("py-pandas")
depends_on("py-openpyxl")
depends_on("python@3.7:3.9")
depends_on("boost")
depends_on("mpich")
depends_on("git", type="build", when="@release")
depends_on("git", type="build", when="@develop")
depends_on("cmake@3.11:", type="build")
depends_on("pkgconfig", type="build")
# TODO: Add timemory and mpip depends_on()
conflicts("+timemory")
# Build failing when added. Creating a conflict as a workaround
conflicts("%gcc@:7.2.0")
conflicts("+mpip -timemory")
conflicts("+mpip -mpi")
def setup_run_environment(self, env):
env.prepend_path("PATH", self.prefix.tools)
env.prepend_path("PATH", self.prefix.bin.tools)
env.set("HICOPS_INSTALL", self.prefix)
env.prepend_path("INCLUDE", self.prefix.include)
def cmake_args(self):
args = [
self.define("USE_MPI", True),
self.define("CMAKE_INSTALL_PREFIX", self.prefix),
self.define_from_variant("USE_TIMEMORY", "timemory"),
self.define_from_variant("USE_MPIP_LIBRARY", "mpip"),
self.define_from_variant("TAILFIT", "tailfit"),
self.define_from_variant("PROGRESS", "progress"),
self.define_from_variant("MAX_SEQ_LEN", "seqlen"),
self.define_from_variant("QALEN", "qalen"),
self.define_from_variant("QCHUNK", "qchunk"),
self.define_from_variant("MAX_HYPERSCORE", "hyperscore"),
self.define_from_variant("MAX_SHDPEAKS", "shdpeaks"),
self.define_from_variant("CMAKE_CXX_STANDARD", "cxx_std"),
]
return args
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