b984adb386
* bowtie: new versions and %gcc@8.0.0: fix Bowtie development shifted from Sourceforge to GitHub. This commit adds several versions from GitHub, using the archive tarballs. Note that the URL for 1.2.2 tarball is actually an '_p1' tag.... It leaves the old 1.2 release download info in place. Versions 1.2.0 and newer come from GitHub (I'm unsure if the 1.2 and 1.2.0 are equivalent). Include a fix that enables %gcc@8.0.0: from: https://github.com/BenLangmead/bowtie/issues/87 But, v1.2.2 has trouble with "newer" gcc's, so it only adds v1.2.2 for %gcc@6.0.0:. Feel free to tighten this. I know that: - 1.2 -> 1.2.2 work with %gcc@5.5.0; - 1.2 -> 1.2.1.1 work with %gcc@8.2.0; and - 1.2.2 fails with %gcc@8.2.0 * Tighten to `conflicts('%gcc@8:', when='@1.2.2')` * Point 1.2.2 and 1.2.2_p1 at the 1.2.2_p1 tarball
60 lines
2.7 KiB
Python
60 lines
2.7 KiB
Python
# Copyright 2013-2019 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 Bowtie(MakefilePackage):
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"""Bowtie is an ultrafast, memory-efficient short read aligner
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for short DNA sequences (reads) from next-gen sequencers."""
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homepage = "https://sourceforge.net/projects/bowtie-bio/"
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url = "https://github.com/BenLangmead/bowtie/archive/v1.2.0.tar.gz"
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# The bowtie project git tagged and GitHub released a v1.2.2,
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# discovered/fixed a bug, git tagged a v1.2.2_p1 and moved the
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# 1.2.2 release to use it rather than making a new `1.2.2_p1`
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# release.
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#
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# We point both of the Spack versions at the same tarball so they
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# build the binaries that are on the release page as v1.2.2
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version('1.2.2_p1', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1')
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version('1.2.2', sha256='e1b02b2e77a0d44a3dd411209fa1f44f0c4ee304ef5cc83f098275085740d5a1', url="https://github.com/BenLangmead/bowtie/archive/v1.2.2_p1.tar.gz")
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version('1.2.1.1', sha256='1b38408b88f61d18d7ff28b2470a8cfeefccb3fc59fd46e4cc62e23874e52c20')
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version('1.2.1', sha256='b2a7c8c879cb08f00a82665bee43e1d4861de44a87912c54d168e44c90869728')
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version('1.2.0', sha256='dc4e7951b8eca56ce7714c47fd4e84f72badd5312ee9546c912af1963570f894')
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# Keeping the old 1.2 version around for reproducibility, it's not
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# clearly identical to 1.2.0.
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version('1.2', md5='6d97f0ea1a65af11d17cc270cfac4af9', url='https://downloads.sourceforge.net/project/bowtie-bio/bowtie/1.2.0/bowtie-1.2-source.zip')
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# Feel free to tighten this. I know that v1.2.2 (aka v1.2.2_p1)
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# builds with %gcc@5.5.5 and fails to build with %gcc@8.2.0. I'm
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# not sure whether or not it works with other versions in the
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# interval.
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conflicts('%gcc@8:', when='@1.2.2:')
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variant('tbb', default=False, description='Use Intel thread building block')
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depends_on('tbb', when='+tbb')
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# See: https://github.com/BenLangmead/bowtie/issues/87, a
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# different fix is in the FreeBSD ports/package tree
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# https://svnweb.freebsd.org/ports?view=revision&revision=483954
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patch('issue-87.patch', when='%gcc@8.0.0:')
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def edit(self, spec, prefix):
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makefile = FileFilter('Makefile')
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makefile.filter('CC = .*', 'CC = ' + env['CC'])
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makefile.filter('CXX = .*', 'CPP = ' + env['CXX'])
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def build(self, spec, prefix):
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if '+tbb' in spec:
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make()
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else:
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make('NO_TBB=1')
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def install(self, spec, prefix):
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make('prefix={0}'.format(self.prefix), 'install')
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