black: reformat entire repository with black
This commit is contained in:
Todd Gamblin
@@ -9,104 +9,107 @@
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class Bcftools(AutotoolsPackage):
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"""BCFtools is a set of utilities that manipulate variant calls in the
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Variant Call Format (VCF) and its binary counterpart BCF. All
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commands work transparently with both VCFs and BCFs, both
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uncompressed and BGZF-compressed."""
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Variant Call Format (VCF) and its binary counterpart BCF. All
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commands work transparently with both VCFs and BCFs, both
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uncompressed and BGZF-compressed."""
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homepage = "https://samtools.github.io/bcftools/"
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url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
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url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
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version('1.14', sha256='b7ef88ae89fcb55658c5bea2e8cb8e756b055e13860036d6be13756782aa19cb')
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version('1.13', sha256='13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90')
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version('1.12', sha256='7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5')
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version('1.10.2', sha256='f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c')
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version('1.9', sha256='6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8')
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version('1.8', sha256='4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced')
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version('1.7', sha256='dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1')
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version('1.6', sha256='293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982')
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version('1.4', sha256='8fb1b0a47ed4e1f9d7c70129d7993aa650da1688fd931b10646d1c4707ae234d')
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version('1.3.1', sha256='12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924')
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version('1.2', sha256='53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6')
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version("1.14", sha256="b7ef88ae89fcb55658c5bea2e8cb8e756b055e13860036d6be13756782aa19cb")
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version("1.13", sha256="13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90")
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version("1.12", sha256="7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5")
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version("1.10.2", sha256="f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c")
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version("1.9", sha256="6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8")
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version("1.8", sha256="4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced")
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version("1.7", sha256="dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1")
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version("1.6", sha256="293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982")
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version("1.4", sha256="8fb1b0a47ed4e1f9d7c70129d7993aa650da1688fd931b10646d1c4707ae234d")
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version("1.3.1", sha256="12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924")
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version("1.2", sha256="53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6")
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variant('libgsl',
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default=False,
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description='build options that require the GNU scientific '
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'library')
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variant(
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"libgsl",
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default=False,
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description="build options that require the GNU scientific " "library",
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)
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variant('perl-filters',
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default=False,
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description='build in support for PERL scripts in -i/-e '
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'filtering expressions, for versions >= 1.8.')
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variant(
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"perl-filters",
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default=False,
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description="build in support for PERL scripts in -i/-e "
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"filtering expressions, for versions >= 1.8.",
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)
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depends_on('gsl', when='+libgsl')
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depends_on('py-matplotlib', when='@1.6:', type='run')
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depends_on('perl', when='@1.8:~perl-filters', type='run')
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depends_on('perl', when='@1.8:+perl-filters', type=('build', 'run'))
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depends_on("gsl", when="+libgsl")
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depends_on("py-matplotlib", when="@1.6:", type="run")
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depends_on("perl", when="@1.8:~perl-filters", type="run")
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depends_on("perl", when="@1.8:+perl-filters", type=("build", "run"))
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depends_on('htslib@1.14', when='@1.14')
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depends_on('htslib@1.13', when='@1.13')
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depends_on('htslib@1.12', when='@1.12')
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depends_on('htslib@1.10.2', when='@1.10.2')
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depends_on('htslib@1.9', when='@1.9')
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depends_on('htslib@1.8', when='@1.8')
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depends_on('htslib@1.7', when='@1.7')
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depends_on('htslib@1.6', when='@1.6')
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depends_on('htslib@1.4', when='@1.4')
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depends_on('htslib@1.3.1', when='@1.3.1')
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depends_on('htslib@1.2', when='@1.2')
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depends_on("htslib@1.14", when="@1.14")
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depends_on("htslib@1.13", when="@1.13")
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depends_on("htslib@1.12", when="@1.12")
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depends_on("htslib@1.10.2", when="@1.10.2")
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depends_on("htslib@1.9", when="@1.9")
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depends_on("htslib@1.8", when="@1.8")
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depends_on("htslib@1.7", when="@1.7")
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depends_on("htslib@1.6", when="@1.6")
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depends_on("htslib@1.4", when="@1.4")
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depends_on("htslib@1.3.1", when="@1.3.1")
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depends_on("htslib@1.2", when="@1.2")
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patch('makefile_12.patch', when='@1.2')
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patch('fix_mk.patch', when='@1.2')
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patch('makefile_13.patch', when='@1.3')
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patch('makefile_14.patch', when='@1.4')
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patch('guess-ploidy.py_2to3.patch', when='@1.6:1.9')
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patch("makefile_12.patch", when="@1.2")
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patch("fix_mk.patch", when="@1.2")
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patch("makefile_13.patch", when="@1.3")
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patch("makefile_14.patch", when="@1.4")
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patch("guess-ploidy.py_2to3.patch", when="@1.6:1.9")
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@when('@1.5:')
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@when("@1.5:")
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def configure_args(self):
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args = []
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args.append('--with-htslib={0}'.format(self.spec['htslib'].prefix))
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args.extend(self.enable_or_disable('libgsl'))
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args.append("--with-htslib={0}".format(self.spec["htslib"].prefix))
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args.extend(self.enable_or_disable("libgsl"))
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if self.spec.satisfies('@1.8:'):
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args.extend(self.enable_or_disable('perl-filters'))
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if self.spec.satisfies("@1.8:"):
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args.extend(self.enable_or_disable("perl-filters"))
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return args
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@when('@1.2:1.4')
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@when("@1.2:1.4")
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def set_make_options(self):
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options = []
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options.append('prefix={0}'.format(self.prefix))
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options.append('HTSDIR={0}'.format(self.spec['htslib'].prefix))
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options.append("prefix={0}".format(self.prefix))
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options.append("HTSDIR={0}".format(self.spec["htslib"].prefix))
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if '+libgsl' in self.spec:
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options.append('USE_GPL=1')
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if "+libgsl" in self.spec:
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options.append("USE_GPL=1")
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return options
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@when('@1.2:1.4')
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@when("@1.2:1.4")
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def autoreconf(self, spec, prefix):
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touch('configure')
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touch("configure")
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@when('@1.2:1.4')
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@when("@1.2:1.4")
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def configure(self, spec, prefix):
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pass
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@when('@1.2:1.4')
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@when("@1.2:1.4")
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def build(self, spec, prefix):
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make_options = self.set_make_options()
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make(*make_options)
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@when('@1.2:1.4')
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@when("@1.2:1.4")
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def install(self, spec, prefix):
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make_options = self.set_make_options()
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make('install', *make_options)
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make("install", *make_options)
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if spec.satisfies('@1.2'):
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if spec.satisfies("@1.2"):
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mkdirp(self.prefix.libexec.bcftools)
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install('plugins/*.so', self.prefix.libexec.bcftools)
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install("plugins/*.so", self.prefix.libexec.bcftools)
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@when('@1.2')
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@when("@1.2")
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def setup_run_environment(self, env):
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env.set('BCFTOOLS_PLUGINS', self.prefix.libexec.bcftools)
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env.set("BCFTOOLS_PLUGINS", self.prefix.libexec.bcftools)
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