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delly2: updating to v0.9.1 (#28000)

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snehring 2021-12-15 23:47:11 -06:00 committed by GitHub
parent 315f01fc96
commit 89044ff5d5
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1 changed files with 29 additions and 17 deletions
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46
var/spack/repos/builtin/packages/delly2/package.py
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@ -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)