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| author | snehring <snehring@users.noreply.github.com> | 2021-12-15 23:47:11 -0600 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2021-12-16 06:47:11 +0100 |
| commit | 89044ff5d560496b742148594edf718d9c485eb6 (patch) | |
| tree | 4b499e6296d552a6b443559f35c6fa324f18b5a7 /var | |
| parent | 315f01fc96637723e99b0cb698fa7e8e34716bd3 (diff) | |
| download | spack-89044ff5d560496b742148594edf718d9c485eb6.tar.gz spack-89044ff5d560496b742148594edf718d9c485eb6.tar.bz2 spack-89044ff5d560496b742148594edf718d9c485eb6.tar.xz spack-89044ff5d560496b742148594edf718d9c485eb6.zip | |
delly2: updating to v0.9.1 (#28000)
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/delly2/package.py | 46 |
1 files changed, 29 insertions, 17 deletions
diff --git a/var/spack/repos/builtin/packages/delly2/package.py b/var/spack/repos/builtin/packages/delly2/package.py index a674d4e17d..3690a086b9 100644 --- a/var/spack/repos/builtin/packages/delly2/package.py +++ b/var/spack/repos/builtin/packages/delly2/package.py @@ -15,31 +15,43 @@ class Delly2(MakefilePackage): homepage = "https://github.com/dellytools/delly" git = "https://github.com/dellytools/delly.git" - version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc') + version('0.9.1', tag='v0.9.1') + version('2017-08-03', commit='e32a9cd55c7e3df5a6ae4a91f31a0deb354529fc', deprecated=True) - depends_on('htslib') - depends_on('boost') - depends_on('bcftools') + variant('openmp', default=False, description='Build with openmp support') + + depends_on('htslib', type=('build', 'link')) + depends_on('boost', type=('build', 'link')) + depends_on('bcftools', type='run') def edit(self, spec, prefix): + if '+openmp' in self.spec: + env['PARALLEL'] = '1' # Only want to build delly source, not submodules. Build fails # using provided submodules, succeeds with existing spack recipes. - makefile = FileFilter('Makefile') - makefile.filter('HTSLIBSOURCES =', '#HTSLIBSOURCES') - makefile.filter('BOOSTSOURCES =', '#BOOSTSOURCES') - makefile.filter('SEQTK_ROOT ?=', '#SEQTK_ROOT') - makefile.filter('BOOST_ROOT ?=', '#BOOST_ROOT') - makefile.filter('cd src', '# cd src') - makefile.filter('.htslib ', '') - makefile.filter('.bcftools ', '') - makefile.filter('.boost ', '') - makefile.filter('.htslib:', '# .htslib:') - makefile.filter('.bcftools:', '# .bcftools:') - makefile.filter('.boost:', '# .boost:') + if self.spec.satisfies('@2017-08-03'): + makefile = FileFilter('Makefile') + makefile.filter('HTSLIBSOURCES =', '#HTSLIBSOURCES') + makefile.filter('BOOSTSOURCES =', '#BOOSTSOURCES') + makefile.filter('SEQTK_ROOT ?=', '#SEQTK_ROOT') + makefile.filter('BOOST_ROOT ?=', '#BOOST_ROOT') + makefile.filter('cd src', '# cd src') + makefile.filter('.htslib ', '') + makefile.filter('.bcftools ', '') + makefile.filter('.boost ', '') + makefile.filter('.htslib:', '# .htslib:') + makefile.filter('.bcftools:', '# .bcftools:') + makefile.filter('.boost:', '# .boost:') + else: + env['EBROOTHTSLIB'] = self.spec['htslib'].prefix + filter_file('BUILT_PROGRAMS =.*$', + 'BUILT_PROGRAMS = src/delly src/dpe', 'Makefile') + filter_file('${SUBMODULES}', '', 'Makefile', string=True) def install(self, spec, prefix): mkdirp(prefix.bin) with working_dir('src'): install('delly', prefix.bin) install('dpe', prefix.bin) - install('cov', prefix.bin) + if self.spec.satisfies('@2017-08-03'): + install('cov', prefix.bin) |