{bio}[GCCcore/12.3.0] chopper v0.9.0

easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb

@@ -0,0 +1,315 @@
+easyblock = 'Cargo'
+
+name = 'chopper'
+version = '0.9.0'
+
+homepage = 'https://github.com/wdecoster/chopper'
+description = """Rust implementation of NanoFilt+NanoLyse, both
+originally written in Python. This tool, intended for long read
+sequencing such as PacBio or ONT, filters and trims a fastq file.
+Filtering is done on average read quality and minimal or maximal read
+length, and applying a headcrop (start of read) and tailcrop (end of
+read) while printing the reads passing the filter."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
+
+github_account = 'wdecoster'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = [
+    'chopper-0.9.0_fix_incorrect_version.patch',
+]
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+    {'windows_i686_msvc-0.52.5.tar.gz': 'db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf'},
+    {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'},
+    {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'},
+    {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'},
+    {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'},
+    {'chopper-0.9.0_fix_incorrect_version.patch': 'b3f3dfa620fbda6d00a73eafc8508a73ac4d96f6edfb0e804b3ff0bc149e37cd'},
+]
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.26.3'),
+    ('Rust', '1.75.0'),
+]
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.4.2'),
+]
+
+crates = [
+    ('adler', '1.0.2'),
+    ('aho-corasick', '1.1.3'),
+    ('anstream', '0.6.13'),
+    ('anstyle', '1.0.6'),
+    ('anstyle-parse', '0.2.3'),
+    ('anstyle-query', '1.0.2'),
+    ('anstyle-wincon', '3.0.2'),
+    ('anyhow', '1.0.82'),
+    ('approx', '0.5.1'),
+    ('atty', '0.2.14'),
+    ('autocfg', '1.2.0'),
+    ('bio', '1.6.0'),
+    ('bio-types', '1.0.1'),
+    ('bit-set', '0.5.3'),
+    ('bit-vec', '0.6.3'),
+    ('buffer-redux', '1.0.1'),
+    ('bv', '0.11.1'),
+    ('bytecount', '0.6.8'),
+    ('bytemuck', '1.15.0'),
+    ('byteorder', '1.5.0'),
+    ('bzip2', '0.4.4'),
+    ('bzip2-sys', '0.1.11+1.0.8'),
+    ('cc', '1.0.94'),
+    ('cfg-if', '1.0.0'),
+    ('clap', '4.5.4'),
+    ('clap_builder', '4.5.2'),
+    ('clap_derive', '4.5.4'),
+    ('clap_lex', '0.7.0'),
+    ('cmake', '0.1.50'),
+    ('colorchoice', '1.0.0'),
+    ('crc32fast', '1.4.0'),
+    ('crossbeam-deque', '0.8.5'),
+    ('crossbeam-epoch', '0.9.18'),
+    ('crossbeam-utils', '0.8.19'),
+    ('csv', '1.3.0'),
+    ('csv-core', '0.1.11'),
+    ('custom_derive', '0.1.7'),
+    ('derive-new', '0.5.9'),
+    ('editdistancek', '1.0.2'),
+    ('either', '1.11.0'),
+    ('enum-map', '2.7.3'),
+    ('enum-map-derive', '0.17.0'),
+    ('equivalent', '1.0.1'),
+    ('feature-probe', '0.1.1'),
+    ('fixedbitset', '0.4.2'),
+    ('flate2', '1.0.28'),
+    ('fxhash', '0.2.1'),
+    ('getrandom', '0.2.14'),
+    ('hashbrown', '0.14.3'),
+    ('heck', '0.4.1'),
+    ('heck', '0.5.0'),
+    ('hermit-abi', '0.1.19'),
+    ('indexmap', '2.2.6'),
+    ('itertools', '0.11.0'),
+    ('itertools-num', '0.1.3'),
+    ('itoa', '1.0.11'),
+    ('lazy_static', '1.4.0'),
+    ('libc', '0.2.153'),
+    ('libm', '0.2.8'),
+    ('libz-ng-sys', '1.1.15'),
+    ('libz-sys', '1.1.16'),
+    ('lzma-sys', '0.1.20'),
+    ('matrixmultiply', '0.3.8'),
+    ('memchr', '2.7.2'),
+    ('minimap2', '0.1.17+minimap2.2.27'),
+    ('minimap2-sys', '0.1.18+minimap2.2.27'),
+    ('miniz_oxide', '0.7.2'),
+    ('multimap', '0.9.1'),
+    ('nalgebra', '0.29.0'),
+    ('nalgebra-macros', '0.1.0'),
+    ('ndarray', '0.15.6'),
+    ('needletail', '0.5.1'),
+    ('newtype_derive', '0.1.6'),
+    ('num-complex', '0.4.5'),
+    ('num-integer', '0.1.46'),
+    ('num-rational', '0.4.1'),
+    ('num-traits', '0.2.18'),
+    ('ordered-float', '3.9.2'),
+    ('paste', '1.0.14'),
+    ('petgraph', '0.6.4'),
+    ('pkg-config', '0.3.30'),
+    ('ppv-lite86', '0.2.17'),
+    ('proc-macro2', '1.0.81'),
+    ('quote', '1.0.36'),
+    ('rand', '0.8.5'),
+    ('rand_chacha', '0.3.1'),
+    ('rand_core', '0.6.4'),
+    ('rand_distr', '0.4.3'),
+    ('rawpointer', '0.2.1'),
+    ('rayon', '1.10.0'),
+    ('rayon-core', '1.12.1'),
+    ('regex', '1.10.4'),
+    ('regex-automata', '0.4.6'),
+    ('regex-syntax', '0.8.3'),
+    ('rustc_version', '0.1.7'),
+    ('rustversion', '1.0.15'),
+    ('ryu', '1.0.17'),
+    ('safe_arch', '0.7.1'),
+    ('semver', '0.1.20'),
+    ('serde', '1.0.198'),
+    ('serde_derive', '1.0.198'),
+    ('simba', '0.6.0'),
+    ('simdutf8', '0.1.4'),
+    ('statrs', '0.16.0'),
+    ('strsim', '0.11.1'),
+    ('strum', '0.25.0'),
+    ('strum_macros', '0.25.3'),
+    ('syn', '1.0.109'),
+    ('syn', '2.0.60'),
+    ('thiserror', '1.0.58'),
+    ('thiserror-impl', '1.0.58'),
+    ('triple_accel', '0.4.0'),
+    ('typenum', '1.17.0'),
+    ('unicode-ident', '1.0.12'),
+    ('utf8parse', '0.2.1'),
+    ('vcpkg', '0.2.15'),
+    ('vec_map', '0.8.2'),
+    ('wasi', '0.11.0+wasi-snapshot-preview1'),
+    ('wide', '0.7.16'),
+    ('winapi', '0.3.9'),
+    ('winapi-i686-pc-windows-gnu', '0.4.0'),
+    ('winapi-x86_64-pc-windows-gnu', '0.4.0'),
+    ('windows-sys', '0.52.0'),
+    ('windows-targets', '0.52.5'),
+    ('windows_aarch64_gnullvm', '0.52.5'),
+    ('windows_aarch64_msvc', '0.52.5'),
+    ('windows_i686_gnu', '0.52.5'),
+    ('windows_i686_gnullvm', '0.52.5'),
+    ('windows_i686_msvc', '0.52.5'),
+    ('windows_x86_64_gnu', '0.52.5'),
+    ('windows_x86_64_gnullvm', '0.52.5'),
+    ('windows_x86_64_msvc', '0.52.5'),
+    ('xz2', '0.1.7'),
+]
+sanity_check_paths = {
+    'files': ['bin/chopper'],
+    'dirs': [],
+}
+
+sanity_check_commands = [
+    'chopper --help',
+]
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch

@@ -0,0 +1,28 @@
+Fix incorrect version number in the 0.9.0 tar file.
+
+Åke Sandgren, 2024-09-16
+diff --git a/Cargo.lock b/Cargo.lock
+index 3e8f1fe..53fa5da 100644
+--- a/Cargo.lock
++++ b/Cargo.lock
+@@ -236,7 +236,7 @@ checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
+
+ [[package]]
+ name = "chopper"
+-version = "0.8.0"
++version = "0.9.0"
+ dependencies = [
+  "approx",
+  "atty",
+diff --git a/Cargo.toml b/Cargo.toml
+index f268dce..7f7277a 100644
+--- a/Cargo.toml
++++ b/Cargo.toml
+@@ -1,6 +1,6 @@
+ [package]
+ name = "chopper"
+-version = "0.8.0"
++version = "0.9.0"
+ authors = ["wdecoster <decosterwouter@gmail.com>"]
+ edition = "2021"
+