diff options
| author | Toyohisa Kameyama <kameyama@riken.jp> | 2019-07-12 12:04:22 +0900 |
|---|---|---|
| committer | Adam J. Stewart <ajstewart426@gmail.com> | 2019-07-11 22:04:22 -0500 |
| commit | 4288dac35bebffe4f576f448389a382f053b17b5 (patch) | |
| tree | 9f9a36b25b4a9e82970c6df7ba6204c6a286fa55 | |
| parent | ea9ac3ee52e10cf2f2edc2109ea1658f433022c6 (diff) | |
| download | spack-4288dac35bebffe4f576f448389a382f053b17b5.tar.gz spack-4288dac35bebffe4f576f448389a382f053b17b5.tar.bz2 spack-4288dac35bebffe4f576f448389a382f053b17b5.tar.xz spack-4288dac35bebffe4f576f448389a382f053b17b5.zip | |
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.
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/package.py | 15 |
1 files changed, 14 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py index 8c72582140..8f00d1ddf9 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -14,6 +14,7 @@ class Bowtie2(Package): 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" + version('2.3.5.1', sha256='335c8dafb1487a4a9228ef922fbce4fffba3ce8bc211e2d7085aac092155a53f') version('2.3.5', sha256='2b6b2c46fbb5565ba6206b47d07ece8754b295714522149d92acebefef08347b') version('2.3.4.1', '8371bbb6eb02ae99c5cf633054265cb9') 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('bowtie2-2.3.1.patch', when='@2.3.1', 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 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') def filter_sbang(self): @@ -55,7 +65,10 @@ class Bowtie2(Package): filter_file(match, substitute, *files, **kwargs) 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) for bow in glob("bowtie2*"): install(bow, prefix.bin) |