Bonito-0.3.5-fosscuda-2019b-Python-3.7.4.eb

easyblock = 'PythonBundle'

name = 'Bonito'
version = '0.3.5'
versionsuffix = '-Python-%(pyver)s'

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

toolchain = {'name': 'fosscuda', 'version': '2019b'}

dependencies = [
    ('Python', '3.7.4'),
    ('PyTorch', '1.3.1', versionsuffix),
    ('h5py', '2.10.0', versionsuffix),
    ('Mako', '1.1.0'),
    ('PyYAML', '5.1.2'),
    ('python-parasail', '1.2', versionsuffix),
    ('tqdm', '4.41.1'),
    ('apex', '20200325', versionsuffix),
    ('minimap2', '2.17'),
    ('CuPy', '8.2.0', versionsuffix),
]

use_pip = True

exts_list = [
    ('toml', '0.10.2', {
        'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'],
    }),
    ('python-editor', '1.0.4', {
        'modulename': 'editor',
        'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'],
    }),
    ('alembic', '1.5.3', {
        'checksums': ['04608b6904a6e6bd1af83e1a48f73f50ba214aeddef44b92d498df33818654a8'],
    }),
    ('cmd2', '1.5.0', {
        'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'],
    }),
    ('prettytable', '0.7.2', {
        'checksums': ['2d5460dc9db74a32bcc8f9f67de68b2c4f4d2f01fa3bd518764c69156d9cacd9'],
    }),
    ('cliff', '3.6.0', {
        'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ",
        'checksums': ['a3f4fa67eeafbcfa7cf9fe4b1755d410876528e1d0d115740db00b50a1250272'],
    }),
    ('colorlog', '4.7.2', {
        'checksums': ['18d05b616438a75762d7d214b9ec3b05d274466c9f3ddd92807e755840c88251'],
    }),
    ('SQLAlchemy', '1.3.23', {
        'checksums': ['6fca33672578666f657c131552c4ef8979c1606e494f78cd5199742dfb26918b'],
    }),
    ('cmaes', '0.7.1', {
        'checksums': ['6476e07392b13b4de581b38fb98322b4fc9affdb5457c5f0f046a7b0bde18767'],
    }),
    ('optuna', '1.5.0', {
        'checksums': ['a8847e0d13364a7e95a7dee31035a1811a2b1395feb2cf98cce7e62affb529df'],
    }),
    ('colorama', '0.4.4', {
        'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'],
    }),
    ('pyperclip', '1.8.1', {
        'checksums': ['9abef1e79ce635eb62309ecae02dfb5a3eb952fa7d6dce09c1aef063f81424d3'],
    }),
    ('importlib_metadata', '2.1.1', {
        'checksums': ['b8de9eff2b35fb037368f28a7df1df4e6436f578fa74423505b6c6a778d5b5dd'],
    }),
    ('stevedore', '3.3.0', {
        'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'],
    }),
    ('progressbar33', '2.4', {
        'modulename': 'progressbar',
        'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'],
    }),
    ('ont-fast5-api', '3.2.0', {
        'checksums': ['24c05250a4ee5262a3a986196ac83b51bc30e1215d90c6f0a595acb5599962e1'],
    }),
    ('fast-ctc-decode', '0.2.5', {
        'source_tmpl': 'fast_ctc_decode-%(version)s-cp37-cp37m-manylinux1_x86_64.whl',
        'unpack_sources': False,
        'checksums': ['b47976b2f951dade427a2f9ddc0ae6905561a76411941cf02b7f6e3e037f4062'],
    }),
    ('mappy', '2.17', {
        'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'],
    }),
    ('seqdist', '0.0.3', {
        'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && ",
        'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'],
    }),
    ('crf-beam', '0.0.1a0', {
        'modulename': 'kbeam',
        'sources': ['crf_beam-%(version)s-cp37-cp37m-manylinux1_x86_64.whl'],
        'unpack_sources': False,
        'checksums': ['81036ec7efd28b5d7bc758ece04c7a7c582164618744dfb64eae29352ba3e8c8'],
    }),
    ('ont-bonito', version, {
        'modulename': 'bonito',
        'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && export PATH=%(installdir)s/bin:$PATH && ",
        'checksums': ['e280df29a5de76494a29c98f3c4946d7108f3014bfaeda214eb54a937c380335'],
    }),
]

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'