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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)
import glob
from spack.package import *
class PyAlphafold(PythonPackage, CudaPackage):
"""AlphaFold is an AI system developed by DeepMind that predicts a
protein's 3D structure from its amino acid sequence. It regularly
achieves accuracy competitive with experiment."""
homepage = "https://github.com/deepmind/alphafold"
url = "https://github.com/deepmind/alphafold/archive/refs/tags/v2.1.1.tar.gz"
maintainers("aweits")
license("Apache-2.0")
version("2.2.4", sha256="8d756e16f6dc7897331d834aade8493820d0ff6a03bf60ce511bac4756c1b1e8")
version("2.1.1", sha256="1adb6e213ba9ac321fc1acb1c563ba9b4fc054c1cebe1191bc0e2aaa671dadf7")
conflicts("platform=darwin", msg="alphafold is only supported on Linux")
# lots of hints on versions and patching taken from docker/Dockerfile
# and requirements.txt
depends_on("python@3.7:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-absl-py@0.13.0:", type=("build", "run"), when="@2.1.1")
depends_on("py-absl-py@1.0.0:", type=("build", "run"), when="@2.2.4")
depends_on("py-biopython@1.79:", type=("build", "run"))
depends_on("py-chex@0.0.7:", type=("build", "run"))
depends_on("py-dm-haiku@0.0.4:", type=("build", "run"), when="@2.1.1")
depends_on("py-dm-haiku@0.0.7:", type=("build", "run"), when="@2.2.4")
depends_on("py-dm-tree@0.1.6:", type=("build", "run"))
depends_on("py-docker", type=("build", "run"))
depends_on("py-immutabledict@2.0.0:", type=("build", "run"))
depends_on("py-jax@0.2.14:", type=("build", "run"), when="@2.1.1")
depends_on("py-jax@0.3.17:", type=("build", "run"), when="@2.2.4")
depends_on("py-ml-collections@0.1.0:", type=("build", "run"))
depends_on("py-numpy@1.19.5:", type=("build", "run"), when="@2.1.1")
depends_on("py-numpy@1.21.6:", type=("build", "run"), when="@2.2.4")
depends_on("py-pandas@1.3.4:", type=("build", "run"))
depends_on("py-protobuf@3.19:", type=("build", "run"), when="@2.2.4")
depends_on("py-scipy@1.7.0:", type=("build", "run"))
depends_on("py-pdbfixer@1.7", type=("build", "run"))
depends_on("py-tensorflow@2.5:", type=("build", "run"), when="@2.1.1")
depends_on("py-tensorflow@2.9:", type=("build", "run"), when="@2.2.4")
depends_on(
"openmm@7.5.1+cuda",
type="run",
patches=[
patch(
"https://raw.githubusercontent.com/deepmind/alphafold/main/docker/openmm.patch",
sha256="a5a0ced820f3ecc56ae634c3111f80614863559b0587954a2658c8d4b2a07ae3",
working_dir="wrappers/python",
level=0,
)
],
)
depends_on("hmmer", type="run")
depends_on("kalign", type="run")
depends_on("hh-suite", type="run")
depends_on("aria2", type="run")
resource(
name="chemprops",
url="https://git.scicore.unibas.ch/schwede/openstructure/-/raw/7102c63615b64735c4941278d92b554ec94415f8/modules/mol/alg/src/stereo_chemical_props.txt",
destination="",
sha256="24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451",
expand=False,
placement="chemprops",
)
@run_after("install")
def install_scripts(self):
mkdirp(self.prefix.bin)
shebang = "#!{0}\n".format(self.spec["python"].command)
for fname in glob.glob("run_alphafold*.py"):
destfile = join_path(self.prefix.bin, fname)
with open(fname, "r") as src:
srcdata = src.read()
with open(destfile, "w") as dest:
dest.write(shebang + srcdata)
set_executable(destfile)
python_dir = join_path(self.prefix, python_platlib, "alphafold", "common")
install("chemprops/stereo_chemical_props.txt", python_dir)
install_tree("scripts", self.prefix.scripts)
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