From 89044ff5d560496b742148594edf718d9c485eb6 Mon Sep 17 00:00:00 2001 From: snehring Date: Wed, 15 Dec 2021 23:47:11 -0600 Subject: delly2: updating to v0.9.1 (#28000) --- var/spack/repos/builtin/packages/delly2/package.py | 46 ++++++++++++++-------- 1 file 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) -- cgit v1.2.3-60-g2f50