From 04a1c44abd4ae39fe02e815110731f22aa055bdc Mon Sep 17 00:00:00 2001
From: Ake Sandgren <ake.sandgren@hpc2n.umu.se>
Date: Mon, 16 Sep 2024 10:25:51 +0200
Subject: [PATCH 1/2] adding easyconfigs: chopper-0.9.0-GCCcore-12.3.0.eb and
 patches: chopper-0.9.0_fix_incorrect_version.patch

---
 .../c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb | 316 ++++++++++++++++++
 .../chopper-0.9.0_fix_incorrect_version.patch |  28 ++
 2 files changed, 344 insertions(+)
 create mode 100644 easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb
 create mode 100644 easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch

diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb
new file mode 100644
index 00000000000..df0b3abaa21
--- /dev/null
+++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb
@@ -0,0 +1,316 @@
+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',
+]
+checksums = [
+    {'v0.9.0.tar.gz': 'ae5b6f8f5ffde45582998b63cb45b4221b25ee37a9fde7a256e653c7f3f12075'},
+    {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'},
+    {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'},
+    {'anstream-0.6.13.tar.gz': 'd96bd03f33fe50a863e394ee9718a706f988b9079b20c3784fb726e7678b62fb'},
+    {'anstyle-1.0.6.tar.gz': '8901269c6307e8d93993578286ac0edf7f195079ffff5ebdeea6a59ffb7e36bc'},
+    {'anstyle-parse-0.2.3.tar.gz': 'c75ac65da39e5fe5ab759307499ddad880d724eed2f6ce5b5e8a26f4f387928c'},
+    {'anstyle-query-1.0.2.tar.gz': 'e28923312444cdd728e4738b3f9c9cac739500909bb3d3c94b43551b16517648'},
+    {'anstyle-wincon-3.0.2.tar.gz': '1cd54b81ec8d6180e24654d0b371ad22fc3dd083b6ff8ba325b72e00c87660a7'},
+    {'anyhow-1.0.82.tar.gz': 'f538837af36e6f6a9be0faa67f9a314f8119e4e4b5867c6ab40ed60360142519'},
+    {'approx-0.5.1.tar.gz': 'cab112f0a86d568ea0e627cc1d6be74a1e9cd55214684db5561995f6dad897c6'},
+    {'atty-0.2.14.tar.gz': 'd9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8'},
+    {'autocfg-1.2.0.tar.gz': 'f1fdabc7756949593fe60f30ec81974b613357de856987752631dea1e3394c80'},
+    {'bio-1.6.0.tar.gz': '7a72cb93babf08c85b375c2938ac678cc637936b3ebb72266d433cec2577f6c2'},
+    {'bio-types-1.0.1.tar.gz': '9d45749b87f21808051025e9bf714d14ff4627f9d8ca967eade6946ea769aa4a'},
+    {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'},
+    {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'},
+    {'buffer-redux-1.0.1.tar.gz': '4c9f8ddd22e0a12391d1e7ada69ec3b0da1914f1cec39c5cf977143c5b2854f5'},
+    {'bv-0.11.1.tar.gz': '8834bb1d8ee5dc048ee3124f2c7c1afcc6bc9aed03f11e9dfd8c69470a5db340'},
+    {'bytecount-0.6.8.tar.gz': '5ce89b21cab1437276d2650d57e971f9d548a2d9037cc231abdc0562b97498ce'},
+    {'bytemuck-1.15.0.tar.gz': '5d6d68c57235a3a081186990eca2867354726650f42f7516ca50c28d6281fd15'},
+    {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'},
+    {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'},
+    {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'},
+    {'cc-1.0.94.tar.gz': '17f6e324229dc011159fcc089755d1e2e216a90d43a7dea6853ca740b84f35e7'},
+    {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'},
+    {'clap-4.5.4.tar.gz': '90bc066a67923782aa8515dbaea16946c5bcc5addbd668bb80af688e53e548a0'},
+    {'clap_builder-4.5.2.tar.gz': 'ae129e2e766ae0ec03484e609954119f123cc1fe650337e155d03b022f24f7b4'},
+    {'clap_derive-4.5.4.tar.gz': '528131438037fd55894f62d6e9f068b8f45ac57ffa77517819645d10aed04f64'},
+    {'clap_lex-0.7.0.tar.gz': '98cc8fbded0c607b7ba9dd60cd98df59af97e84d24e49c8557331cfc26d301ce'},
+    {'cmake-0.1.50.tar.gz': 'a31c789563b815f77f4250caee12365734369f942439b7defd71e18a48197130'},
+    {'colorchoice-1.0.0.tar.gz': 'acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7'},
+    {'crc32fast-1.4.0.tar.gz': 'b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa'},
+    {'crossbeam-deque-0.8.5.tar.gz': '613f8cc01fe9cf1a3eb3d7f488fd2fa8388403e97039e2f73692932e291a770d'},
+    {'crossbeam-epoch-0.9.18.tar.gz': '5b82ac4a3c2ca9c3460964f020e1402edd5753411d7737aa39c3714ad1b5420e'},
+    {'crossbeam-utils-0.8.19.tar.gz': '248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345'},
+    {'csv-1.3.0.tar.gz': 'ac574ff4d437a7b5ad237ef331c17ccca63c46479e5b5453eb8e10bb99a759fe'},
+    {'csv-core-0.1.11.tar.gz': '5efa2b3d7902f4b634a20cae3c9c4e6209dc4779feb6863329607560143efa70'},
+    {'custom_derive-0.1.7.tar.gz': 'ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9'},
+    {'derive-new-0.5.9.tar.gz': '3418329ca0ad70234b9735dc4ceed10af4df60eff9c8e7b06cb5e520d92c3535'},
+    {'editdistancek-1.0.2.tar.gz': '3e02df23d5b1c6f9e69fa603b890378123b93073df998a21e6e33b9db0a32613'},
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+    {'enum-map-2.7.3.tar.gz': '6866f3bfdf8207509a033af1a75a7b08abda06bbaaeae6669323fd5a097df2e9'},
+    {'enum-map-derive-0.17.0.tar.gz': 'f282cfdfe92516eb26c2af8589c274c7c17681f5ecc03c18255fe741c6aa64eb'},
+    {'equivalent-1.0.1.tar.gz': '5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5'},
+    {'feature-probe-0.1.1.tar.gz': '835a3dc7d1ec9e75e2b5fb4ba75396837112d2060b03f7d43bc1897c7f7211da'},
+    {'fixedbitset-0.4.2.tar.gz': '0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80'},
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+    {'fxhash-0.2.1.tar.gz': 'c31b6d751ae2c7f11320402d34e41349dd1016f8d5d45e48c4312bc8625af50c'},
+    {'getrandom-0.2.14.tar.gz': '94b22e06ecb0110981051723910cbf0b5f5e09a2062dd7663334ee79a9d1286c'},
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+    {'heck-0.5.0.tar.gz': '2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea'},
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+    {'lazy_static-1.4.0.tar.gz': 'e2abad23fbc42b3700f2f279844dc832adb2b2eb069b2df918f455c4e18cc646'},
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+    {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'},
+    {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'},
+    {'windows_aarch64_gnullvm-0.52.5.tar.gz': '7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263'},
+    {'windows_aarch64_msvc-0.52.5.tar.gz': '9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6'},
+    {'windows_i686_gnu-0.52.5.tar.gz': '88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670'},
+    {'windows_i686_gnullvm-0.52.5.tar.gz': '87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9'},
+    {'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'
diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch b/easybuild/easyconfigs/c/chopper/chopper-0.9.0_fix_incorrect_version.patch
new file mode 100644
index 00000000000..57c15b94db4
--- /dev/null
+++ b/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"
+ 

From 4f82480bbc82b2912a3befb929eb044719d0034e Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 17 Sep 2024 09:29:54 +0200
Subject: [PATCH 2/2] remove whitespace from empty line in chopper easyconfig

---
 easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb
index df0b3abaa21..b1788fb34f9 100644
--- a/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb
+++ b/easybuild/easyconfigs/c/chopper/chopper-0.9.0-GCCcore-12.3.0.eb
@@ -303,7 +303,6 @@ crates = [
     ('windows_x86_64_msvc', '0.52.5'),
     ('xz2', '0.1.7'),
 ]
- 
 sanity_check_paths = {
     'files': ['bin/chopper'],
     'dirs': [],