7b9f8abce5
Add language dependencies `c`, `cxx`, and `fortran`. These `depends_on` statements are auto-generated based on file extensions found in source tarballs/zipfiles. The `# generated` comment can be removed by package maintainers after validating correctness.
61 lines
2.4 KiB
Python
61 lines
2.4 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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from spack.pkg.builtin.boost import Boost
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class Lordec(MakefilePackage):
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"""LoRDEC is a program to correct sequencing errors in long reads from
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3rd generation sequencing with high error rate, and is especially
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intended for PacBio reads."""
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homepage = "http://www.atgc-montpellier.fr/lordec/"
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url = "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz"
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license("CECILL-2.1")
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version("0.9", sha256="8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b")
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version("0.8", sha256="3894a7c57649a3545b598f92a48d55eda66d729ab51606b00470c50611b12823")
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depends_on("cxx", type="build") # generated
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def url_for_version(self, version):
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if version == Version("0.8"):
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return "https://gite.lirmm.fr/lordec/lordec-releases/uploads/e3116a5f251e46e47f7a3b7ddb2bd7f6/lordec-src_0.8.tar.gz"
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if version == Version("0.9"):
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return "https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/lordec-src_0.9.tar.bz2"
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depends_on("boost@1.48.0:1.64.0", type=["build", "link"])
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# TODO: replace this with an explicit list of components of Boost,
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# for instance depends_on('boost +filesystem')
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# See https://github.com/spack/spack/pull/22303 for reference
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depends_on(Boost.with_default_variants)
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depends_on("gatb-core@1.4.1:", type=["build", "link", "run"])
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depends_on("zlib-api", type=["build", "link"])
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build_targets = ["clean", "all"]
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def edit(self, spec, prefix):
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lbstr = "AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no"
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filter_file("^AUTOMATIC_LIBBOOST_LOCAL_INSTALL.*$", lbstr, "Makefile")
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filter_file("gatb_v.*gatb_core.hpp", "", "Makefile")
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def install(self, spec, prefix):
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mkdir(prefix.include)
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install("*.h", prefix.include)
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mkdir(prefix.bin)
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binaries = [
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"lordec-correct",
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"lordec-stat",
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"lordec-trim",
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"lordec-trim-split",
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"lordec-build-SR-graph",
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]
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for binary in binaries:
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install(binary, prefix.bin)
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mkdir(prefix.tools)
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install("lordec_sge_slurm_wrapper.sh", prefix.tools)
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