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bowtie2: Add version 2.5.3.1 and fix to build on ARM (#11974)

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* 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.
This commit is contained in:
Toyohisa Kameyama 2019-07-12 12:04:22 +09:00 committed by Adam J. Stewart
parent ea9ac3ee52
commit 4288dac35b
1 changed files with 14 additions and 1 deletions
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15
var/spack/repos/builtin/packages/bowtie2/package.py
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@ -14,6 +14,7 @@ class Bowtie2(Package):
homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml" homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml"
url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip" url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.3.1/bowtie2-2.3.1-source.zip"
version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f')
version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b') version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b')
version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9') version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9')
version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478') version('2.3.1', 'b4efa22612e98e0c23de3d2c9f2f2478')
@ -29,9 +30,18 @@ class Bowtie2(Package):
patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0) patch('bowtie2-2.2.5.patch', when='@2.2.5', level=0)
patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0) patch('bowtie2-2.3.1.patch', when='@2.3.1', level=0)
patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0) patch('bowtie2-2.3.0.patch', when='@2.3.0', level=0)
resource(name='simde', git="https://github.com/nemequ/simde",
destination='.', when='target=aarch64')
# seems to have trouble with 6's -std=gnu++14 # seems to have trouble with 6's -std=gnu++14
conflicts('%gcc@6:', when='@:2.3.1') conflicts('%gcc@6:', when='@:2.3.1')
conflicts('@:2.3.5.0', when='target=aarch64')
def patch(self):
if self.spec.satisfies('target=aarch64'):
copy_tree('simde', 'third_party/simde')
if self.spec.satisfies('%gcc@:4.8.9 target=aarch64'):
filter_file('-fopenmp-simd', '', 'Makefile')
@run_before('install') @run_before('install')
def filter_sbang(self): def filter_sbang(self):
@ -55,7 +65,10 @@ def filter_sbang(self):
filter_file(match, substitute, *files, **kwargs) filter_file(match, substitute, *files, **kwargs)
def install(self, spec, prefix): def install(self, spec, prefix):
make() make_arg = []
if self.spec.satisfies('target=aarch64'):
make_arg.append('POPCNT_CAPABILITY=0')
make(*make_arg)
mkdirp(prefix.bin) mkdirp(prefix.bin)
for bow in glob("bowtie2*"): for bow in glob("bowtie2*"):
install(bow, prefix.bin) install(bow, prefix.bin)