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adding easyconfigs: purge_dups-1.2.6-foss-2023b.eb
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akesandgren committed Dec 9, 2024
1 parent 05fb1bd commit e26bc12
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85 changes: 85 additions & 0 deletions easybuild/easyconfigs/p/purge_dups/purge_dups-1.2.6-foss-2023b.eb
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easyblock = 'PythonBundle'

name = 'purge_dups'
version = '1.2.6'

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

toolchain = {'name': 'foss', 'version': '2023b'}

builddependencies = [
('pybind11', '2.11.1'),
]

dependencies = [
('zlib', '1.2.13'),
('bzip2', '1.0.8'),
('Python', '3.11.5'),
('matplotlib', '3.8.2'),
('minimap2', '2.28'),
]

use_pip = True

default_easyblock = 'MakeCp'

components = [
(name, version, {
'source_urls': ['https://github.com/dfguan/purge_dups/archive'],
'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}],
'checksums': ['75b20df834d28410858ccd4e2d65b6c70849f3cbe5fc05959f38bfc2d041c704'],
'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}],
'patches': [{
'name': 'KMC_use_EB_pybind11_and_libs.patch',
'sourcepath': 'KMC-c05a5f9fd94683248ebe04484a60f86792cf328f',
}],
'checksums': [
'7251941f4b1913bfdd68759d9292b419d95fe7c63815056e15ecb097a12a0bc4',
'2f54971aae26787777d0e4b638a9682bd4bc22cbf3fda170c7baf4c610808ac9',
],
'prebuildopts': 'cd KMC-* && ',
'buildopts': 'CC="$CXX"',
'files_to_copy': [(['KMC-*/bin/*kmc*'], 'bin'), 'KMC-*/spectra.py'],
}),
]

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

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'

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