bowtie2: Add version 2.5.3.1 and fix to build on ARM (#11974)
* bowtie2: Add version 2.5.3.1 and fix to build on ARM 1. Add version 2.5.3.1. 2. Add simde for ARM. 3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM. 4. Add Makefile option POPCNT_CAPABILITY=0 for ARM. * flake8.
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@ -14,6 +14,7 @@ class Bowtie2(Package):
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homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
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url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
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version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
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version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
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version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9')
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version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
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@ -29,9 +30,18 @@ class Bowtie2(Package):
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patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
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patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
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patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
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resource(name='simde', git="https://github.com/nemequ/simde",
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destination='.', when='target=aarch64')
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# seems to have trouble with 6's -std=gnu++14
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conflicts('%gcc@6:', when='@:2.3.1')
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conflicts('@:2.3.5.0', when='target=aarch64')
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def patch(self):
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if self.spec.satisfies('target=aarch64'):
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copy_tree('simde', 'third_party/simde')
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if self.spec.satisfies('%gcc@:4.8.9 target=aarch64'):
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filter_file('-fopenmp-simd', '', 'Makefile')
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@run_before('install')
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def filter_sbang(self):
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@ -55,7 +65,10 @@ def filter_sbang(self):
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filter_file(match, substitute, *files, **kwargs)
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def install(self, spec, prefix):
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make()
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make_arg = []
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if self.spec.satisfies('target=aarch64'):
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make_arg.append('POPCNT_CAPABILITY=0')
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make(*make_arg)
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mkdirp(prefix.bin)
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for bow in glob("bowtie2*"):
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install(bow, prefix.bin)
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