a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
104 lines
3.8 KiB
Python
104 lines
3.8 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
|
|
# Spack Project Developers. See the top-level COPYRIGHT file for details.
|
|
#
|
|
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
|
|
|
|
|
class Bcftools(AutotoolsPackage):
|
|
"""BCFtools is a set of utilities that manipulate variant calls in the
|
|
Variant Call Format (VCF) and its binary counterpart BCF. All
|
|
commands work transparently with both VCFs and BCFs, both
|
|
uncompressed and BGZF-compressed."""
|
|
|
|
homepage = "http://samtools.github.io/bcftools/"
|
|
url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
|
|
|
|
version('1.10.2', sha256='f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c')
|
|
version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8')
|
|
version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced')
|
|
version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1')
|
|
version('1.6', sha256='293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982')
|
|
version('1.4', sha256='8fb1b0a47ed4e1f9d7c70129d7993aa650da1688fd931b10646d1c4707ae234d')
|
|
version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924')
|
|
version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6')
|
|
|
|
variant('libgsl',
|
|
default=False,
|
|
description='build options that require the GNU scientific '
|
|
'library')
|
|
|
|
variant('perl-filters',
|
|
default=False,
|
|
description='build in support for PERL scripts in -i/-e '
|
|
'filtering expressions, for versions >= 1.8.')
|
|
|
|
depends_on('gsl', when='+libgsl')
|
|
depends_on('py-matplotlib', when='@1.6:', type='run')
|
|
depends_on('perl', when='@1.8:~perl-filters', type='run')
|
|
depends_on('perl', when='@1.8:+perl-filters', type=('build', 'run'))
|
|
|
|
depends_on('htslib@1.10.2', when='@1.10.2')
|
|
depends_on('htslib@1.9', when='@1.9')
|
|
depends_on('htslib@1.8', when='@1.8')
|
|
depends_on('htslib@1.7', when='@1.7')
|
|
depends_on('htslib@1.6', when='@1.6')
|
|
depends_on('htslib@1.4', when='@1.4')
|
|
depends_on('htslib@1.3.1', when='@1.3.1')
|
|
depends_on('htslib@1.2', when='@1.2')
|
|
|
|
patch('makefile_12.patch', when='@1.2')
|
|
patch('fix_mk.patch', when='@1.2')
|
|
patch('makefile_13.patch', when='@1.3')
|
|
patch('makefile_14.patch', when='@1.4')
|
|
patch('guess-ploidy.py_2to3.patch', when='@1.6:1.9')
|
|
|
|
@when('@1.5:')
|
|
def configure_args(self):
|
|
args = []
|
|
|
|
args.append('--with-htslib={0}'.format(self.spec['htslib'].prefix))
|
|
args.extend(self.enable_or_disable('libgsl'))
|
|
|
|
if self.spec.satisfies('@1.8:'):
|
|
args.extend(self.enable_or_disable('perl-filters'))
|
|
|
|
return args
|
|
|
|
@when('@1.2:1.4')
|
|
def set_make_options(self):
|
|
options = []
|
|
|
|
options.append('prefix={0}'.format(self.prefix))
|
|
options.append('HTSDIR={0}'.format(self.spec['htslib'].prefix))
|
|
|
|
if '+libgsl' in self.spec:
|
|
options.append('USE_GPL=1')
|
|
|
|
return options
|
|
|
|
@when('@1.2:1.4')
|
|
def autoreconf(self, spec, prefix):
|
|
touch('configure')
|
|
|
|
@when('@1.2:1.4')
|
|
def configure(self, spec, prefix):
|
|
pass
|
|
|
|
@when('@1.2:1.4')
|
|
def build(self, spec, prefix):
|
|
make_options = self.set_make_options()
|
|
make(*make_options)
|
|
|
|
@when('@1.2:1.4')
|
|
def install(self, spec, prefix):
|
|
make_options = self.set_make_options()
|
|
make('install', *make_options)
|
|
|
|
if spec.satisfies('@1.2'):
|
|
mkdirp(self.prefix.libexec.bcftools)
|
|
install('plugins/*.so', self.prefix.libexec.bcftools)
|
|
|
|
@when('@1.2')
|
|
def setup_run_environment(self, env):
|
|
env.set('BCFTOOLS_PLUGINS', self.prefix.libexec.bcftools)
|