Bonito-0.3.8-fosscuda-2020b.eb

easyblock = 'PythonBundle'

name = 'Bonito'
version = '0.3.8'

homepage = 'https://github.com/nanoporetech/bonito'
description = "Convolution Basecaller for Oxford Nanopore Reads"

toolchain = {'name': 'fosscuda', 'version': '2020b'}

dependencies = [
    ('Python', '3.8.6'),
    ('SciPy-bundle', '2020.11'),
    ('PyTorch', '1.7.1'),
    ('h5py', '3.1.0'),
    ('Mako', '1.1.3'),
    ('PyYAML', '5.3.1'),
    ('python-parasail', '1.2.4'),
    ('tqdm', '4.56.2'),
    ('apex', '20210420'),
    ('minimap2', '2.18'),
    ('CuPy', '8.5.0'),
]

use_pip = True

exts_list = [
    ('python-editor', '1.0.4', {
        'modulename': 'editor',
        'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'],
    }),
    ('alembic', '1.5.8', {
        'checksums': ['e27fd67732c97a1c370c33169ef4578cf96436fa0e7dcfaeeef4a917d0737d56'],
    }),
    ('cmd2', '1.5.0', {
        'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'],
    }),
    ('prettytable', '2.1.0', {
        'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'],
    }),
    ('cliff', '3.7.0', {
        'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ",
        'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'],
    }),
    ('colorlog', '5.0.1', {
        'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'],
    }),
    ('greenlet', '1.0.0', {
        'checksums': ['719e169c79255816cdcf6dccd9ed2d089a72a9f6c42273aae12d55e8d35bdcf8'],
    }),
    ('SQLAlchemy', '1.4.11', {
        'checksums': ['4ad4044eb86fbcbdff2106e44f479fbdac703d77860b3e19988c8a8786e73061'],
    }),
    ('cmaes', '0.8.2', {
        'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'],
    }),
    ('optuna', '2.7.0', {
        'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'],
    }),
    ('colorama', '0.4.4', {
        'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'],
    }),
    ('pyperclip', '1.8.2', {
        'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'],
    }),
    ('importlib_metadata', '4.0.1', {
        'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'],
    }),
    ('stevedore', '3.3.0', {
        'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'],
    }),
    ('progressbar33', '2.4', {
        'modulename': 'progressbar',
        'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'],
    }),
    ('ont-fast5-api', '3.3.0', {
        'checksums': ['8ccbf8d203ba90c2757f25b6bbcfb0e5c90bbbb9972f2e19c3f6d6d9943d9f15'],
    }),
    ('fast-ctc-decode', '0.3.0', {
        'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl',
        'unpack_sources': False,
        'checksums': ['623d83f8de5e02199a09bfe0160a1e477f0db8d4ab612b26a7e42c2a335b378c'],
    }),
    ('mappy', '2.18', {
        'checksums': ['18fffdb4b831cc3f5399b919b0942c640bf9a943ca22102ac446f53af3b905a8'],
    }),
    ('seqdist', '0.0.3', {
        'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ",
        'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'],
    }),
    ('crf-beam', '0.0.1a0', {
        'modulename': 'kbeam',
        'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'],
        'unpack_sources': False,
        'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'],
    }),
    ('ont-bonito', version, {
        'modulename': 'bonito',
        'preinstallopts': "sed -i 's/[><=]=.*//g' requirements.txt && export PATH=%(installdir)s/bin:$PATH && ",
        'checksums': ['f18ec073c841bb0ccfe9049530df370ab0fb19931614e8ba37316acaa58639a1'],
    }),
]

sanity_pip_check = True

sanity_check_paths = {
    'files': ['bin/bonito'],
    'dirs': ['lib/python%(pyshortver)s/site-packages'],
}

sanity_check_commands = [
    "bonito --help",
    "bonito convert --help",
    "bonito download --help",
]

moduleclass = 'bio'