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#453 subset-bam from master
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pavelToman committed Nov 14, 2024
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1 change: 0 additions & 1 deletion 453_trusTEr/subset-bam.eb
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Expand Up @@ -385,7 +385,6 @@ sanity_check_paths = {

sanity_check_commands = ["subset-bam --help"]


moduleclass = 'bio'

# E1:
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309 changes: 309 additions & 0 deletions 453_trusTEr/subset-bam_master.eb
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# Author: J. Sassmannshausen (Imperial College London/UK)
# Update: Pavel Tománek (Inuits)

easyblock = 'Cargo'

name = 'subset-bam'
version = '1.1.0-20230907'
local_commit = 'c135329'

homepage = 'https://github.com/10XGenomics/subset-bam'
description = """subset-bam is a tool to subset a 10x Genomics BAM file based on a tag,
most commonly the cell barcode tag."""

toolchain = {'name': 'GCCcore', 'version': '12.3.0'}

source_urls = ['https://github.com/10XGenomics/subset-bam/archive/']
sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
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]

builddependencies = [
('binutils', '2.40'),
('Rust', '1.75.0'),
('Clang', '16.0.6'),
]

dependencies = [('bzip2', '1.0.8')]

crates = [
('addr2line', '0.12.1'),
('adler32', '1.1.0'),
('aho-corasick', '0.6.10'),
('aho-corasick', '0.7.10'),
('ansi_term', '0.11.0'),
('arrayref', '0.3.6'),
('arrayvec', '0.5.1'),
('atty', '0.2.14'),
('autocfg', '1.0.0'),
('backtrace', '0.3.49'),
('base64', '0.11.0'),
('bindgen', '0.36.1'),
('bitflags', '0.9.1'),
('bitflags', '1.2.1'),
('blake2b_simd', '0.5.10'),
('bstr', '0.2.13'),
('byteorder', '1.3.4'),
('cc', '1.0.54'),
('cexpr', '0.2.3'),
('cfg-if', '0.1.10'),
('chrono', '0.4.11'),
('clang-sys', '0.22.0'),
('clap', '2.33.1'),
('constant_time_eq', '0.1.5'),
('crossbeam-deque', '0.7.3'),
('crossbeam-epoch', '0.8.2'),
('crossbeam-queue', '0.2.3'),
('crossbeam-utils', '0.7.2'),
('csv', '1.1.3'),
('csv-core', '0.1.10'),
('custom_derive', '0.1.7'),
('data-encoding', '2.2.1'),
('dirs', '1.0.5'),
('either', '1.5.3'),
('env_logger', '0.5.13'),
('faccess', '0.2.4'),
('failure', '0.1.8'),
('failure_derive', '0.1.8'),
('fs-utils', '1.1.4'),
('getrandom', '0.1.14'),
('gimli', '0.21.0'),
('glob', '0.2.11'),
('hermit-abi', '0.1.14'),
('human-panic', '1.0.3'),
('humantime', '1.3.0'),
('idna', '0.1.5'),
('ieee754', '0.2.6'),
('itertools', '0.6.5'),
('itoa', '0.4.6'),
('lazy_static', '0.2.11'),
('lazy_static', '1.4.0'),
('libc', '0.2.71'),
('libloading', '0.5.2'),
('linear-map', '1.2.0'),
('log', '0.4.19'),
('matches', '0.1.8'),
('maybe-uninit', '2.0.0'),
('memchr', '1.0.2'),
('memchr', '2.3.3'),
('memoffset', '0.5.4'),
('miniz_oxide', '0.3.7'),
('newtype_derive', '0.1.6'),
('nom', '3.2.1'),
('num-integer', '0.1.43'),
('num-traits', '0.2.12'),
('num_cpus', '1.13.0'),
('object', '0.20.0'),
('os_type', '2.2.0'),
('peeking_take_while', '0.1.2'),
('percent-encoding', '1.0.1'),
('ppv-lite86', '0.2.8'),
('proc-macro2', '0.3.5'),
('proc-macro2', '1.0.18'),
('quick-error', '1.2.3'),
('quote', '0.5.2'),
('quote', '1.0.7'),
('rand', '0.7.3'),
('rand_chacha', '0.2.2'),
('rand_core', '0.5.1'),
('rand_hc', '0.2.0'),
('rayon', '1.3.1'),
('rayon-core', '1.7.1'),
('redox_syscall', '0.1.56'),
('redox_users', '0.3.4'),
('regex', '0.2.11'),
('regex', '1.3.9'),
('regex-automata', '0.1.9'),
('regex-syntax', '0.5.6'),
('regex-syntax', '0.6.18'),
('remove_dir_all', '0.5.3'),
('ring', '0.14.6'),
('rust-argon2', '0.7.0'),
('rust-htslib', '0.20.0'),
('rustc-demangle', '0.1.16'),
('rustc_version', '0.1.7'),
('ryu', '1.0.5'),
('scopeguard', '1.1.0'),
('semver', '0.1.20'),
('serde', '1.0.113'),
('serde_derive', '1.0.113'),
('simplelog', '0.5.3'),
('spin', '0.5.2'),
('strsim', '0.8.0'),
('syn', '1.0.31'),
('synstructure', '0.12.4'),
('tempfile', '3.1.0'),
('term', '0.5.2'),
('termcolor', '1.1.0'),
('terminal_size', '0.1.12'),
('textwrap', '0.11.0'),
('thread_local', '0.3.6'),
('thread_local', '1.0.1'),
('time', '0.1.43'),
('tinyvec', '0.3.3'),
('toml', '0.5.6'),
('ucd-util', '0.1.8'),
('unicode-bidi', '0.3.4'),
('unicode-normalization', '0.1.13'),
('unicode-width', '0.1.7'),
('unicode-xid', '0.1.0'),
('unicode-xid', '0.2.0'),
('untrusted', '0.6.2'),
('url', '1.7.2'),
('utf8-ranges', '1.0.4'),
('uuid', '0.8.1'),
('vec_map', '0.8.2'),
('wasi', '0.9.0+wasi-snapshot-preview1'),
('which', '1.0.5'),
('winapi', '0.3.8'),
('winapi-i686-pc-windows-gnu', '0.4.0'),
('winapi-util', '0.1.5'),
('winapi-x86_64-pc-windows-gnu', '0.4.0'),
]

# It looks like we need to specify this as else it will not work.
# buildopts = '-Z unstable-options '
# testopts = '-Z unstable-options '
# installopts = '-Z unstable-options '

sanity_check_paths = {
'files': ['bin/subset-bam'],
'dirs': [],
}

sanity_check_commands = ["subset-bam --help"]

moduleclass = 'bio'

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