Commit 51986677 authored by Rodrigo Osorio's avatar Rodrigo Osorio
Browse files

biology/p5-TrimGalore: update 0.6.11->2.2.0 and move to biology/TrimGalore 

Changelog:
    https://github.com/FelixKrueger/TrimGalore/releases/tag/v2.1.0
    https://github.com/FelixKrueger/TrimGalore/releases/tag/v2.2.0

Since v2 TrimGalore was rewrote in Rust, the migration notes give
details about what stays the same and what's new in v2.

https://www.trimgalore.com/reference/migration/

Major changes;
    * not a perl port anymore
    * no dependency (FastQC bundled via fastqc-rust)

Take maintainership for this port
parent 7c5dcd59

MOVED

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@@ -5314,3 +5314,4 @@ deskutils/gnome-shell-extension-panel-osd||2026-05-18|Marked broken and abandone 
deskutils/gnome-shell-extension-mediaplayer||2026-05-18|Marked broken and upstream repo is archived

devel/rubygem-rugged17|devel/rubygem-rugged|2026-05-24|Use devel/rubygem-rugged instead

www/rubygem-deckar01-task_list-gitlab|www/rubygem-deckar01-task_list|2026-05-24|Use www/rubygem-deckar01-task_list instead

biology/p5-TrimGalore|biology/TrimGalore|2026-05-24|After V2.0 Trim Galore was rewrite in rust

biology/Makefile

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@@ -3,6 +3,7 @@ 
    SUBDIR += R-cran-Biobase

    SUBDIR += R-cran-BiocGenerics

    SUBDIR += R-cran-BiocManager

    SUBDIR += TrimGalore

    SUBDIR += abyss

    SUBDIR += ad2vcf

    SUBDIR += andi
@@ -143,7 +144,6 @@ 
    SUBDIR += p5-Bio-Variation

    SUBDIR += p5-BioPerl

    SUBDIR += p5-BioPerl-Run

    SUBDIR += p5-TrimGalore

    SUBDIR += p5-transdecoder

    SUBDIR += paml

    SUBDIR += pbbam

biology/TrimGalore/Makefile

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PORTNAME=	TrimGalore

DISTVERSIONPREFIX=	v

DISTVERSION=	2.2.0

CATEGORIES=	biology



MAINTAINER=	rodrigo@FreeBSD.org

COMMENT=	Consistent quality and adapter trimming for next-generation sequencing data

WWW=		https://github.com/FelixKrueger/TrimGalore



LICENSE=	GPLv3

LICENSE_FILE=	${WRKSRC}/LICENSE



USES=		cargo



USE_GITHUB=	yes

GH_ACCOUNT=	FelixKrueger



.include <bsd.port.mk>

biology/TrimGalore/Makefile.crates

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CARGO_CRATES=	adler2-2.0.1 \

		aes-0.8.4 \

		aho-corasick-1.1.4 \

		android_system_properties-0.1.5 \

		anstream-1.0.0 \

		anstyle-1.0.14 \

		anstyle-parse-1.0.0 \

		anstyle-query-1.1.5 \

		anstyle-wincon-3.0.11 \

		anyhow-1.0.102 \

		approx-0.5.1 \

		arbitrary-1.4.2 \

		arrayref-0.3.9 \

		arrayvec-0.7.6 \

		autocfg-1.5.0 \

		base64-0.22.1 \

		bit-vec-0.8.0 \

		bitflags-2.11.1 \

		block-buffer-0.10.4 \

		bstr-1.12.1 \

		bumpalo-3.20.2 \

		bytemuck-1.25.0 \

		byteorder-1.5.0 \

		byteorder-lite-0.1.0 \

		bytes-1.11.1 \

		bzip2-0.5.2 \

		bzip2-rs-0.1.2 \

		bzip2-sys-0.1.13+1.0.8 \

		cc-1.2.61 \

		cfg-if-1.0.4 \

		chrono-0.4.44 \

		cipher-0.4.4 \

		clap-4.6.1 \

		clap_builder-4.6.0 \

		clap_derive-4.6.1 \

		clap_lex-1.1.0 \

		color_quant-1.1.0 \

		colorchoice-1.0.5 \

		constant_time_eq-0.3.1 \

		core-foundation-sys-0.8.7 \

		core_affinity-0.8.3 \

		core_maths-0.1.1 \

		cpufeatures-0.2.17 \

		crc-3.4.0 \

		crc-catalog-2.5.0 \

		crc32fast-1.5.0 \

		crossbeam-channel-0.5.15 \

		crossbeam-deque-0.8.6 \

		crossbeam-epoch-0.9.18 \

		crossbeam-utils-0.8.21 \

		crypto-common-0.1.7 \

		data-url-0.3.2 \

		deflate64-0.1.12 \

		deranged-0.5.8 \

		derive_arbitrary-1.4.2 \

		digest-0.10.7 \

		displaydoc-0.2.5 \

		either-1.15.0 \

		env_filter-1.0.1 \

		env_logger-0.11.10 \

		equivalent-1.0.2 \

		euclid-0.22.14 \

		fastqc-rust-1.0.1 \

		fdeflate-0.3.7 \

		find-msvc-tools-0.1.9 \

		flate2-1.1.9 \

		float-cmp-0.9.0 \

		flume-0.11.1 \

		fontconfig-parser-0.5.8 \

		fontdb-0.23.0 \

		futures-core-0.3.32 \

		futures-sink-0.3.32 \

		generic-array-0.14.7 \

		getrandom-0.2.17 \

		getrandom-0.3.4 \

		gif-0.14.2 \

		gzp-2.0.2 \

		hashbrown-0.17.0 \

		hdf5-pure-0.1.1 \

		heck-0.5.0 \

		hermit-abi-0.5.2 \

		hmac-0.12.1 \

		iana-time-zone-0.1.65 \

		iana-time-zone-haiku-0.1.2 \

		image-webp-0.2.4 \

		imagesize-0.14.0 \

		indexmap-2.14.0 \

		inout-0.1.4 \

		is_terminal_polyfill-1.70.2 \

		itoa-1.0.18 \

		jiff-0.2.23 \

		jiff-static-0.2.23 \

		jobserver-0.1.34 \

		js-sys-0.3.95 \

		kurbo-0.13.0 \

		lexical-core-1.0.6 \

		lexical-parse-float-1.0.6 \

		lexical-parse-integer-1.0.6 \

		lexical-util-1.0.7 \

		lexical-write-float-1.0.6 \

		lexical-write-integer-1.0.6 \

		libc-0.2.184 \

		libm-0.2.16 \

		libz-sys-1.1.28 \

		lock_api-0.4.14 \

		log-0.4.29 \

		lzma-rs-0.3.0 \

		lzma-sys-0.1.20 \

		matrixmultiply-0.3.10 \

		memchr-2.8.0 \

		memmap2-0.9.10 \

		miniz_oxide-0.8.9 \

		nalgebra-0.32.6 \

		nalgebra-macros-0.2.2 \

		nanorand-0.7.0 \

		noodles-0.88.0 \

		noodles-bam-0.73.0 \

		noodles-bgzf-0.35.0 \

		noodles-core-0.16.0 \

		noodles-csi-0.42.0 \

		noodles-sam-0.69.0 \

		num-complex-0.4.6 \

		num-conv-0.2.1 \

		num-integer-0.1.46 \

		num-rational-0.4.2 \

		num-traits-0.2.19 \

		num_cpus-1.17.0 \

		once_cell-1.21.4 \

		once_cell_polyfill-1.70.2 \

		paste-1.0.15 \

		pbkdf2-0.12.2 \

		pico-args-0.5.0 \

		pkg-config-0.3.33 \

		png-0.18.1 \

		portable-atomic-1.13.1 \

		portable-atomic-util-0.2.6 \

		powerfmt-0.2.0 \

		ppv-lite86-0.2.21 \

		proc-macro2-1.0.106 \

		quick-error-2.0.1 \

		quote-1.0.45 \

		r-efi-5.3.0 \

		rand-0.8.6 \

		rand_chacha-0.3.1 \

		rand_core-0.6.4 \

		rand_distr-0.4.3 \

		rawpointer-0.2.1 \

		rayon-1.12.0 \

		rayon-core-1.13.0 \

		regex-1.12.3 \

		regex-automata-0.4.14 \

		regex-syntax-0.8.10 \

		resvg-0.47.0 \

		rgb-0.8.53 \

		roxmltree-0.20.0 \

		roxmltree-0.21.1 \

		rustversion-1.0.22 \

		rustybuzz-0.20.1 \

		safe_arch-0.7.4 \

		scopeguard-1.2.0 \

		serde-1.0.228 \

		serde_core-1.0.228 \

		serde_derive-1.0.228 \

		serde_json-1.0.149 \

		sha1-0.10.6 \

		shlex-1.3.0 \

		simba-0.8.1 \

		simd-adler32-0.3.9 \

		simplecss-0.2.2 \

		siphasher-1.0.2 \

		slotmap-1.1.1 \

		smallvec-1.15.1 \

		spin-0.9.8 \

		statrs-0.17.1 \

		strict-num-0.1.1 \

		strsim-0.11.1 \

		subtle-2.6.1 \

		svgtypes-0.16.1 \

		syn-2.0.117 \

		thiserror-2.0.18 \

		thiserror-impl-2.0.18 \

		time-0.3.47 \

		time-core-0.1.8 \

		tiny-skia-0.12.0 \

		tiny-skia-path-0.12.0 \

		tinyvec-1.11.0 \

		tinyvec_macros-0.1.1 \

		ttf-parser-0.25.1 \

		typenum-1.20.0 \

		unicode-bidi-0.3.18 \

		unicode-bidi-mirroring-0.4.0 \

		unicode-ccc-0.4.0 \

		unicode-ident-1.0.24 \

		unicode-properties-0.1.4 \

		unicode-script-0.5.8 \

		unicode-vo-0.1.0 \

		usvg-0.47.0 \

		utf8parse-0.2.2 \

		vcpkg-0.2.15 \

		version_check-0.9.5 \

		wasi-0.11.1+wasi-snapshot-preview1 \

		wasip2-1.0.3+wasi-0.2.9 \

		wasm-bindgen-0.2.118 \

		wasm-bindgen-macro-0.2.118 \

		wasm-bindgen-macro-support-0.2.118 \

		wasm-bindgen-shared-0.2.118 \

		weezl-0.1.12 \

		wide-0.7.33 \

		winapi-0.3.9 \

		winapi-i686-pc-windows-gnu-0.4.0 \

		winapi-x86_64-pc-windows-gnu-0.4.0 \

		windows-core-0.62.2 \

		windows-implement-0.60.2 \

		windows-interface-0.59.3 \

		windows-link-0.2.1 \

		windows-result-0.4.1 \

		windows-strings-0.5.1 \

		windows-sys-0.61.2 \

		wit-bindgen-0.57.1 \

		xmlwriter-0.1.0 \

		xz2-0.1.7 \

		zerocopy-0.8.48 \

		zerocopy-derive-0.8.48 \

		zeroize-1.8.2 \

		zeroize_derive-1.4.3 \

		zip-2.4.2 \

		zlib-rs-0.6.3 \

		zmij-1.0.21 \

		zopfli-0.8.3 \

		zstd-0.13.3 \

		zstd-safe-7.2.4 \

		zstd-sys-2.0.16+zstd.1.5.7 \

		zune-core-0.5.1 \

		zune-jpeg-0.5.15

biology/TrimGalore/distinfo

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