72 lines
2.9 KiB
Python
72 lines
2.9 KiB
Python
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Psipred(MakefilePackage):
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"""PSIPRED is a simple and accurate secondary structure prediction method, incorporating
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two feed-forward neural networks which perform an analysis on output obtained from
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PSI-BLAST (Position Specific Iterated - BLAST). Using a very stringent cross validation
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method to evaluate the methods performance"""
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homepage = "http://bioinf.cs.ucl.ac.uk/psipred/"
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url = "http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.02.tar.gz"
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license_url = "http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/LICENSE"
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version("4.02", sha256="b4009b6a5f8b76c6d60ac91c4a743512d844864cf015c492fb6d1dc0d092c467")
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variant("blast-plus", default=False, description="Use blast-plus in place of blast-legacy")
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depends_on("blast-legacy", type="run", when="~blast-plus")
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depends_on("blast-plus", type="run", when="+blast-plus")
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build_directory = "src"
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# patch to fix segfault on input lines >256 chars
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# https://github.com/psipred/psipred/pull/8
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patch(
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"https://github.com/psipred/psipred/commit/cee0f2c.patch?full_index=1",
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sha256="ef75999f688eaf7984e17f663c17c13e4eaba98912a904be128f562a7eaf8315",
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when="@:1.10.1%gcc@13:",
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level=1,
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)
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def edit(self, spec, prefix):
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with working_dir(self.build_directory):
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filter_file(r"CC\s+= cc", f"CC = {spack_cc}", "Makefile")
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def build(self, spec, prefix):
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with working_dir(self.build_directory):
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make("all")
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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with working_dir(self.build_directory):
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for f in ("psipred", "psipass2", "chkparse", "seq2mtx"):
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install(f, prefix.bin)
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@run_after("install")
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def configure(self):
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# install data sources
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install_tree("data", prefix.data)
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# modify and install the relevant helper script examples
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mkdir(self.prefix.scripts)
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if self.spec.satisfies("~blast-plus"):
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script = FileFilter("runpsipred")
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blast_location = self.spec["blast-legacy"].prefix.bin
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else: # +blast-plus
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script = FileFilter(join_path("BLAST+", "runpsipredplus"))
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blast_location = self.spec["blast-plus"].prefix.bin
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script.filter("set dbname .*", "set dbname = ")
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script.filter("set ncbidir .*", f"set ncbidir = {blast_location}")
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script.filter("set execdir .*", f"set execdir = {self.prefix.bin}")
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script.filter("set datadir .*", f"set datadir = {self.prefix.data}")
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if self.spec.satisfies("~blast-plus"):
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install("runpsipred", self.prefix.scripts)
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else: # +blast-plus
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install(join_path("BLAST+", "runpsipredplus"), self.prefix.scripts)
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