diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/vcftools/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/vcftools/package.py | 67 |
1 files changed, 42 insertions, 25 deletions
diff --git a/var/spack/repos/builtin/packages/vcftools/package.py b/var/spack/repos/builtin/packages/vcftools/package.py index e2e9543cd8..92ccb0e152 100644 --- a/var/spack/repos/builtin/packages/vcftools/package.py +++ b/var/spack/repos/builtin/packages/vcftools/package.py @@ -8,48 +8,65 @@ from spack.package import * class Vcftools(AutotoolsPackage): """VCFtools is a program package designed for working with VCF files, - such as those generated by the 1000 Genomes Project. The aim of - VCFtools is to provide easily accessible methods for working - with complex genetic variation data in the form of VCF files. + such as those generated by the 1000 Genomes Project. The aim of + VCFtools is to provide easily accessible methods for working + with complex genetic variation data in the form of VCF files. """ homepage = "https://vcftools.github.io/" - url = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz" + url = "https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz" # this is "a pre-release" # version('0.1.15', sha256='31e47afd5be679d89ece811a227525925b6907cce4af2c86f10f465e080383e3') - version('0.1.14', sha256='76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582') + version("0.1.14", sha256="76d799dd9afcb12f1ed42a07bc2886cd1a989858a4d047f24d91dcf40f608582") - depends_on('perl', type=('build', 'run')) - depends_on('zlib') + depends_on("perl", type=("build", "run")) + depends_on("zlib") # this needs to be in sync with what setup_run_environment adds to # PERL5LIB below def configure_args(self): - return ['--with-pmdir={0}'.format(self.prefix.lib)] + return ["--with-pmdir={0}".format(self.prefix.lib)] - @run_before('install') + @run_before("install") def filter_sbang(self): """Run before install so that the standard Spack sbang install hook - can fix up the path to the perl binary. + can fix up the path to the perl binary. """ - with working_dir('src/perl'): - match = '^#!/usr/bin/env perl' - substitute = "#!{perl}".format(perl=self.spec['perl'].command.path) + with working_dir("src/perl"): + match = "^#!/usr/bin/env perl" + substitute = "#!{perl}".format(perl=self.spec["perl"].command.path) # tab-to-vcf added in 0.1.15 - files = ['fill-aa', 'fill-an-ac', 'fill-fs', - 'fill-ref-md5', 'tab-to-vcf', 'vcf-annotate', - 'vcf-compare', 'vcf-concat', 'vcf-consensus', - 'vcf-contrast', 'vcf-convert', - 'vcf-fix-newlines', 'vcf-fix-ploidy', - 'vcf-indel-stats', 'vcf-isec', 'vcf-merge', - 'vcf-phased-join', 'vcf-query', - 'vcf-shuffle-cols', 'vcf-sort', 'vcf-stats', - 'vcf-subset', 'vcf-to-tab', 'vcf-tstv', - 'vcf-validator', ] - kwargs = {'ignore_absent': True, 'backup': False, 'string': False} + files = [ + "fill-aa", + "fill-an-ac", + "fill-fs", + "fill-ref-md5", + "tab-to-vcf", + "vcf-annotate", + "vcf-compare", + "vcf-concat", + "vcf-consensus", + "vcf-contrast", + "vcf-convert", + "vcf-fix-newlines", + "vcf-fix-ploidy", + "vcf-indel-stats", + "vcf-isec", + "vcf-merge", + "vcf-phased-join", + "vcf-query", + "vcf-shuffle-cols", + "vcf-sort", + "vcf-stats", + "vcf-subset", + "vcf-to-tab", + "vcf-tstv", + "vcf-validator", + ] + kwargs = {"ignore_absent": True, "backup": False, "string": False} filter_file(match, substitute, *files, **kwargs) def setup_run_environment(self, env): - env.prepend_path('PERL5LIB', self.prefix.lib) + env.prepend_path("PERL5LIB", self.prefix.lib) |