diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/bowtie2/package.py | 60 |
1 files changed, 28 insertions, 32 deletions
diff --git a/var/spack/repos/builtin/packages/bowtie2/package.py b/var/spack/repos/builtin/packages/bowtie2/package.py index e09ea00e50..0eab7a3068 100644 --- a/var/spack/repos/builtin/packages/bowtie2/package.py +++ b/var/spack/repos/builtin/packages/bowtie2/package.py @@ -4,7 +4,7 @@ # SPDX-License-Identifier: (Apache-2.0 OR MIT) -class Bowtie2(Package): +class Bowtie2(MakefilePackage): """Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences""" @@ -25,49 +25,45 @@ class Bowtie2(Package): depends_on('perl', type='run') depends_on('python', type='run') depends_on('zlib', when='@2.3.1:') + depends_on('simde', type='link') 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:') conflicts('@2.4.1', when='target=aarch64:') - def patch(self): - if self.spec.target.family == 'aarch64': - copy_tree('simde', 'third_party/simde') - if self.spec.satisfies('%gcc@:4.8.9'): - filter_file('-fopenmp-simd', '', 'Makefile') + def edit(self, spec, prefix): + kwargs = {'ignore_absent': True, 'backup': False, 'string': False} - @run_before('install') - def filter_sbang(self): - """Run before install so that the standard Spack sbang install hook - can fix up the path to the perl|python binary. - """ + match = '^#!/usr/bin/env perl' + perl = spec['perl'].command + substitute = "#!{perl}".format(perl=perl) + files = ['bowtie2', ] + filter_file(match, substitute, *files, **kwargs) - with working_dir(self.stage.source_path): - kwargs = {'ignore_absent': True, 'backup': False, 'string': False} + match = '^#!/usr/bin/env python' + python = spec['python'].command + substitute = "#!{python}".format(python=python) + files = ['bowtie2-build', 'bowtie2-inspect'] + filter_file(match, substitute, *files, **kwargs) - match = '^#!/usr/bin/env perl' - perl = self.spec['perl'].command - substitute = "#!{perl}".format(perl=perl) - files = ['bowtie2', ] - filter_file(match, substitute, *files, **kwargs) + match = '-Ithird_party/simde' + simdepath = spec['simde'].prefix.include + substitute = "-I{simdepath}".format(simdepath=simdepath) + files = ['Makefile'] + filter_file(match, substitute, *files, **kwargs) - match = '^#!/usr/bin/env python' - python = self.spec['python'].command - substitute = "#!{python}".format(python=python) - files = ['bowtie2-build', 'bowtie2-inspect'] - filter_file(match, substitute, *files, **kwargs) - - def install(self, spec, prefix): - make_arg = [] - if self.spec.target.family == 'aarch64': + @property + def build_targets(self): + make_arg = ['PREFIX={0}'.format(self.prefix)] + if self.spec.satisfies('target=aarch64:'): make_arg.append('POPCNT_CAPABILITY=0') - make(*make_arg) - mkdirp(prefix.bin) - install('bowtie2*', prefix.bin) + return make_arg + + @property + def install_targets(self): + return ['PREFIX={0}'.format(self.prefix), 'install'] |