purge_dups-1.2.5-foss-2021b.eb

easyblock = 'PythonBundle'

name = 'purge_dups'
version = '1.2.5'

homepage = 'https://github.com/dfguan/purge_dups'
description = "purge haplotigs and overlaps in an assembly based on read depth"

toolchain = {'name': 'foss', 'version': '2021b'}

dependencies = [
    ('Python', '3.9.6'),
    ('matplotlib', '3.4.3'),
    ('minimap2', '2.22'),
    ('zlib', '1.2.11'),
]

use_pip = True

default_easyblock = 'MakeCp'

components = [
    (name, version, {
        'source_urls': ['https://github.com/dfguan/purge_dups/archive/refs/tags/'],
        'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
        'checksums': ['7879a8ecc26e5de1eaaf4b4633cb240ed2802d648068b193652477317a3e2645'],
        'start_dir': 'purge_dups-%(version)s',
        'prebuildopts': "cd src && ",
        'buildopts': 'CC="$CC" CFLAGS="$CFLAGS"',
        'files_to_copy': ['bin', 'scripts'],
    }),
    ('KMC', '20190629', {
        'source_urls': ['https://github.com/dfguan/KMC/archive/'],
        'sources': [{'download_filename': 'c05a5f9.tar.gz', 'filename': SOURCE_TAR_GZ}],
        'checksums': ['7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4'],
        'prebuildopts': 'cd KMC-* && ',
        'buildopts': 'CC="$CXX"',
        'files_to_copy': [(['KMC-*/bin/*kmc*'], 'bin'), 'KMC-*/spectra.py'],
    }),
]

exts_list = [
    ('runner', '20191220', {
        'sources': [{
            'git_config': {
                'url': 'https://github.com/dfguan/',
                'repo_name': 'runner',
                'commit': '73a4d11',
            },
            'filename': 'runner-%(version)s.tar.gz',
        }],
        'checksums': [None],
        'preinstallopts': "sed -i 's/0.0.0/%(version)s/g' setup.py && "
    }),
]

sanity_check_paths = {
    'files': ['bin/kmc', 'bin/purge_dups'],
    'dirs': ['scripts'],
}

sanity_check_commands = [
    "purge_dups -h 2>&1 | grep 'Program: purge_dups'",
    "kmc --help",
    "run_purge_dups.py -h",
    "hist_plot.py -h",
]

sanity_pip_check = True

modextrapaths = {'PATH': 'scripts'}

moduleclass = 'bio'