[VCFtools] [package list]

VCFtools/0.1.17-cpeGNU-26.03 (VCFtools-0.1.17-cpeGNU-26.03.eb)

Install with the EasyBuild-user module:

eb VCFtools-0.1.17-cpeGNU-26.03.eb -r

To access module help after installation and get reminded for which stacks and partitions the module is installed, use module spider VCFtools/0.1.17-cpeGNU-26.03.

EasyConfig:

easyblock = 'ConfigureMake'

local_Perl_version =         '5.42.0'        # https://www.perl.org/get.html
local_zlib_version =         '2.3.3'         # https://github.com/zlib-ng/zlib-ng/releases

local_HTSlib_version =       '1.24'          # https://github.com/samtools/htslib/releases

local_VCFtools_version =     '0.1.17'        # https://github.com/vcftools/vcftools/releases

name =    'VCFtools'
version = local_VCFtools_version

homepage = "https://vcftools.github.io"

whatis = [
    'Description: VCFtools provides methods for working with VCF files'
]

description = """
The aim of VCFtools is to provide  easily accessible methods for working with
complex genetic variation data in the form of VCF files.
"""

doc_urls = [
   'man page vcftools in section 1'
]

toolchain = {'name': 'cpeGNU', 'version': '26.03'}

source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/']
sources =     ['%(namelower)s-%(version)s.tar.gz']
checksums =   ['b9e0e1c3e86533178edb35e02c6c4de9764324ea0973bebfbb747018c2d2a42c']

build_deps = [
    ('buildtools',          '%(toolchain_version)s', '', True),
    ('craype-network-none', EXTERNAL_MODULE),
    ('craype-accel-none',   EXTERNAL_MODULE),
]

deps = [
    ('Perl',   local_Perl_version),
    ('HTSlib', local_HTSlib_version),
    ('zlib',   local_zlib_version),
]

pre_configure_opts = 'module unload rocm cray-libsci && '
pre_install_opts = pre_test_opts = pre_build_opts = pre_configure_opts

post_install_cmds = [
    'cp -r examples %(installdir)s',
    'mkdir -p %(installdir)s/share/licenses/%(name)s',
    'cp LICENSE README.md %(installdir)s/share/licenses/%(name)s',   
]

env_mod_extra_paths = {
    'PERL5LIB': 'lib/perl5/site_perl'
}

# Note that the test lists only a small subset of the commands.
sanity_check_paths = {
    'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']],
    'dirs':  [f'lib/perl5/site_perl/{local_Perl_version}', 'share/man/man1'],
}

sanity_check_cmds = [ # Cannot easily try the commands as most return error codes for --help.
    'vcftools --version',
]

env_mod_category = 'bio'

[VCFtools] [package list]