spack/var/spack/repos/builtin/packages/vcftools/package.py
Todd Gamblin eea786f4e8 relicense: replace LGPL headers with Apache-2.0/MIT SPDX headers
- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
  - core and most packages are (Apache-2.0 OR MIT)
  - a very small number of remaining packages are LGPL-2.1-only
2018-10-17 14:42:06 -07:00

56 lines
2.3 KiB
Python

# Copyright 2013-2018 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)
from spack 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.
"""
homepage = "https://vcftools.github.io/"
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', '61045197848dea20a0158d2faf02e5be')
version('0.1.14', 'a110662535651caa6cc8c876216a9f77')
depends_on('perl', type=('build', 'run'))
depends_on('zlib')
# this needs to be in sync with what setup_environment adds to
# PERL5LIB below
def configure_args(self):
return ['--with-pmdir={0}'.format(self.prefix.lib)]
@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.
"""
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}
filter_file(match, substitute, *files, **kwargs)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', self.prefix.lib)