1b2638c9b1
* primer3: move to github, add 2.5.0, fix 2.3.7
- The Primer3 project moved to GitHub.
- update the URL
- compare the tarballs 2.3.7 from Sourceforge and github, no
significant differences (e.g. the Sourceforge tarball contained a
couple of "tmp" files).
- update the signature for the 2.3.7 tarball.
- @2.3.7 doesn't build with gcc@8.4.0, there's a dubious pointer/int
comparison that causes an error. It was fixed upstream in newer
versions, apply simple patch to this version so that it continues to
be build-able with newer compilers. See:
- https://github.com/primer3-org/primer3/issues/2
- https://github.com/primer3-org/primer3/issues/3
- Add info for @2.5.0, which builds cleanly.
* Flake8 cleanup
40 lines
1.6 KiB
Python
40 lines
1.6 KiB
Python
# Copyright 2013-2020 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 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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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',
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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',
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'long_seq_tm_test'):
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install(binary, prefix.bin)
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