41 lines
1.7 KiB
Python
41 lines
1.7 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 Primer3(MakefilePackage):
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"""Primer3 is a widely used program for designing PCR primers
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(PCR = "Polymerase Chain Reaction"). PCR is an essential and
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ubiquitous tool in genetics and molecular biology. Primer3
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can also design hybridization probes and sequencing primers."""
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homepage = "https://primer3.org/"
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url = "https://github.com/primer3-org/primer3/archive/v2.3.7.tar.gz"
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license("GPL-2.0-only")
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version("2.6.1", sha256="805cef7ef39607cd40f0f5bb8b32e35e20007153a0a55131dd430ce644c8fb9e")
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version("2.5.0", sha256="7581e2fa3228ef0ee1ffa427b2aa0a18fc635d561208327471daf59d1b804da0")
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version("2.3.7", sha256="f7ac3e64dc89b7c80882bf0f52c2c0a58572f5fdafd178680d4a7ae91b6c465b")
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build_directory = "src"
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# Prior to May 15, 2018, the code contained invalid pointer/int
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# comparisons, leading to compilers that default to strict mode
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# failing to compile thal.c.
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# This prevents building 2.3.7 w/ gcc@8.4.0. Details here:
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# https://github.com/primer3-org/primer3/issues/2
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# https://github.com/primer3-org/primer3/issues/3
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def patch(self):
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if self.spec.version == Version("2.3.7"):
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filter_file(r"^(CC_OPTS.*)", r"\1 -fpermissive", join_path("src", "Makefile"))
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def install(self, spec, prefix):
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with working_dir(self.build_directory):
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mkdirp(prefix.bin)
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for binary in ("primer3_core", "ntdpal", "oligotm", "long_seq_tm_test"):
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install(binary, prefix.bin)
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