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4227 commits

Author SHA1 Message Date
Muhammad Moinur Rahman
93078cd6b2
biology/R-cran-BiocManager: Return to pool 2025-04-27 11:48:13 +02:00
Jason W. Bacon
0bef7dda8c biology/biolibc-tools: Update to 0.1.5 
A few enhancements and updates for libxtend and biolibc APIs
Changes: https://github.com/auerlab/biolibc-tools/releases
 2025-04-26 15:40:24 -05:00
Jason W. Bacon
aa9df88f1c biology/fasda: Update to 0.2.0 
Several enhancements and a few important bug fixes
Changes: https://github.com/auerlab/fasda/releases
 2025-04-26 15:38:22 -05:00
Jason W. Bacon
f680350d5e biology/biolibc: Update to 0.2.7 
Minor fixes and enhancements
Changes: https://github.com/auerlab/biolibc/releases
 2025-04-26 15:35:36 -05:00
Yuri Victorovich
0097ef9a2c biology/{,py-}libsedml: update 2.0.32 → 2.0.33 
Reported by:	portscout
 2025-04-24 00:33:39 -07:00
Rene Ladan
cee4ec23e8 biology/py-orange3-single-cell: fix typo in DEPRECATED 2025-04-21 17:12:02 +02:00
Rene Ladan
49b26d6578 */*orange*: expire (in)direct consumers of misc/py-dictdiffer on 2025-06-21 2025-04-21 17:08:56 +02:00
Jason W. Bacon
cdd5a51ea0 biology/minimap2: Update to 2.29 
A few new features and fixes
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout
 2025-04-20 08:15:13 -05:00
Jason W. Bacon
b3f6f8596d biology/fastp: Update to 0.24.1 
Bug fix release
Changes: https://github.com/OpenGene/fastp/releases

Reported by:    portscout
 2025-04-17 07:51:42 -05:00
Wen Heping
6062197438 biology/R-cran-Biobase: Update to 2.66.0 
Take maintainership

PR:		285994
Reported by:	wen@
Approved by:	maintainer
 2025-04-11 14:28:35 +00:00
Wen Heping
75aaf8aeca biology/R-cran-BiocGenerics: Update to 0.52.0 
Take maintainership

PR:		285994
Reported by:	wen@
Approved by:	maintainer
 2025-04-11 14:28:35 +00:00
Po-Chuan Hsieh
150c0018fd
Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test} 
- Update USE_PYTHON=cython{,_run,_test}
- Convert all cython3 occurrence to USE_PYTHON=cython3*
- While I'm here, fix incorrect usage of combining cython3 in BUILD_DEPENDS and USE_PYTHON=cython

It is added to simplify the future transition from Cython 0.29 to 3.

The minimal version is set to 3.0.12 because it is required by devel/py-propcache.
The upper bound of version is set to 3.1 because it is limited by multiple ports.
 2025-04-09 22:55:11 +08:00
Mikael Urankar
2a5976aebe lang/rust: Bump revisions after 1.86.0 
PR:		285840
 2025-04-08 10:41:13 +02:00
Jason W. Bacon
cc15cab2da biology/fasda-utils: Fast and simple differential analysis extras 
FASDA aims to provide a fast and simple differential analysis tool
that just works and does not require any knowledge beyond basic Unix
command-line skills. The code is written entirely in C to maximize
efficiency and portability, and to provide a simple command-line user
interface.

FASDA-utils is a collection of optional companion programs and
scripts.  They are separated from the main FASDA distribution in order
to keep FASDA packages minimal.
 2025-04-06 06:27:20 -05:00
Yuri Victorovich
3ae41ffa99 biology/py-resdk: update 21.2.1 → 22.0.0 
Reported by:	portscout
 2025-04-02 02:10:43 -07:00
Adam Weinberger
a4e30d4f4f go: Bump ports for go124 update 2025-04-01 22:07:58 -04:00
Rene Ladan
3b5eced32d biology/checkm: expire on 2025-06-01 for science/py-DendroPy 2025-03-31 22:45:34 +02:00
Rene Ladan
4d04ded80f biology/py-orange3-single-cell: expire on 2025-06-01 for math/py-fastdtw 2025-03-31 16:19:33 +02:00
Yuri Victorovich
a63cf26b66 biology/{,py-}libnuml: update 1.1.6 → 1.1.7 
Reported by:	portscout
 2025-03-28 02:54:11 -07:00
Jason W. Bacon
888c0b0e32 biology/subread: Update to 2.1.0 
Improved identification and reporting of junctions in featureCounts
Changes: https://subread.sourceforge.net/
 2025-03-27 17:05:26 -05:00
Muhammad Moinur Rahman
46ed1f693e
biology/seaview: Update version 5.0.5=>5.1 
Changelog: https://doua.prabi.fr/software/seaview_data/CHANGES
 2025-03-26 08:36:45 +01:00
Älven
b66379cdc6 biology/bwa: update 0.7.18 => 0.7.19 
ChangeLog:
https://github.com/lh3/bwa/blob/master/NEWS.md#release-0719-22-march-2025

Notable changes:

 * Bugfix: internal @HD lines. The bug was introduced in 0.7.18.
 * Merged #414, #391, #346, #312, #311, #308, #291, #288, #286 and #212

PR:		285620
Reported by:	alster@vinterdalen.se (maintainer)
 2025-03-26 08:34:34 +01:00
Joseph Mingrone
1367bc51cd
biology/hyphy: Update to 2.5.70 
Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.70
Sponsored by:	The FreeBSD Foundation
 2025-03-23 22:33:03 -03:00
Wen Heping
e3d441848b biology/py-newick: Update to 1.10.0 2025-03-22 13:41:03 +00:00
Jason W. Bacon
a57f4b8dea biology/sra-tools: Update to 3.2.1 
Fix fasterq-dump mkdir error:
https://github.com/ncbi/sra-tools/issues/1016#issuecomment-2737694569
Numerous other fixes and enhancements
Changes: https://github.com/ncbi/sra-tools/commits/master/

Reported by:    portscout
 2025-03-21 06:27:22 -05:00
Jason W. Bacon
da25ff8f31 biology/py-macs3: Unbreak package build 
pep57 -> distutils
Port passed poudriere before, but spontaneously broke due to
other changes

Reported by:    pkg-fallout
 2025-03-19 08:45:50 -05:00
Po-Chuan Hsieh
b9c852a7d6
biology/rubygem-bio: Update to 2.0.6 
Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
 2025-03-19 11:46:26 +08:00
Charlie Li
e87d8134a3
gnome.mk: rename gdkpixbuf2 to gdkpixbuf to prepare for port move 
The GTK 1-based gdk-pixbuf has not existed for some time.

No functional or package changes.
 2025-03-17 00:02:08 -04:00
Yuri Victorovich
a47e9277dc biology/seqkit: update 2.9.0 → 2.10.0 
Reported by:	portscout
 2025-03-13 00:41:22 -07:00
Yuri Victorovich
c3c7d4cb7d biology/taxonkit: update 0.18.0 → 0.19.0 
Reported by:	portscout
 2025-03-13 00:41:20 -07:00
Yuri Victorovich
a28e38f28f biology/ncbi-cxx-toolkit: Broken on i386 
Reported by:	fallout
 2025-03-10 01:13:13 -07:00
Charlie Li
06a08e69f3
python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal 
Any missed ports, feel free to bump.

Any ports that need setuptools at runtime can have the devel/py-setuptools
manually added back to RUN_DEPENDS, but understand that this practice
is deprecated; see CHANGES for details.
 2025-03-07 23:05:21 -05:00
Jason W. Bacon
c2d10be9f2 biology/py-macs3: Update to 3.0.3 
A few new features and bug fixes
Changes: https://github.com/macs3-project/MACS/releases

Reported by:    portscout
 2025-03-07 08:28:52 -06:00
Yuri Victorovich
b8776527e2 biology/ncbi-cxx-toolkit: update 28.0.12 → 29.0.1 
Reported by:	portscout
 2025-03-06 08:51:55 -08:00
Jason W. Bacon
8de761e7d4 biology/ncbi-blast+: Update to 2.16.0_3 
Fix build of seqdb_perf
Disable build system attempts to access NCBI file servers,
causing NFS timeouts where autofs is enabled
 2025-03-06 06:42:48 -06:00
Adam Weinberger
d0642a6176 Bump all go ports for yesterday's releases 2025-03-05 11:02:56 -05:00
Jason W. Bacon
886844b5ec biology/py-crossmap: Update to 0.7.3 
Several fixes and enhancements since 0.5.4
Changes: https://github.com/liguowang/CrossMap/releases

PR:             284923
Reported by:    alster@vinterdalen.se
 2025-03-04 07:12:42 -06:00
Yuri Victorovich
58a5831389 biology/py-pyrodigal: Fix build with scikit-build-core-0.11.0 
Reported by:	fallout
 2025-03-03 12:59:36 -08:00
Jason W. Bacon
84399cefee biology/vsearch: Update to 2.30.0 
Add options --n_mismatch, --fastq_minqual, and --fastq_truncee_rate
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout
 2025-03-02 06:37:09 -06:00
Joseph Mingrone
20f4a2658a
biology/hyphy: Update to 2.5.69 
Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.69actual
Sponsored by:	The FreeBSD Foundation
 2025-03-01 23:52:07 -04:00
Rainer Hurling
483199e803 */*: Bump PORTREVISION after math/nlopt update 2025-03-01 16:09:11 +01:00
Mikael Urankar
cf7c4b037d lang/rust: Bump revisions after 1.85.0 
PR:		284884
 2025-02-24 08:55:52 +01:00
Yuri Victorovich
f066ac192f biology/seqwish: Set OPENMP=OFF and broken where OpenMP isn't available 
Reported by:	fallout
 2025-02-23 11:42:19 -08:00
Jason W. Bacon
d758b1caa1 Multiple biology ports: Replace pypi homepage with github 
portscout apparently can't work with PYPI homepages
 2025-02-21 07:04:08 -06:00
Jason W. Bacon
bac90e855c biology/freebayes: Update to 1.3.9 
Upstream moved away from git submodules to external deps
Several fixes since 1.3.6
Changes: https://github.com/freebayes/freebayes/releases

Reported by:    portscout
 2025-02-18 14:45:11 -06:00
Älven
fc3ebf9794 biology/py-orange3-bioinformatics: Update 4.3.1 → 4.8.4 
Changelogs:
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.4.0
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.5.0
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.6.0
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.7.0
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.7.1
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.7.2
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.8.0
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.8.1
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.8.2
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.8.3
https://github.com/biolab/orange3-bioinformatics/releases/tag/4.8.4

Cosmetic changes in Makefile.

PR:		279307
Approved by:	yuri (maintainer, timeout > 8 months)
 2025-02-18 22:45:18 +03:00
Jason W. Bacon
813f71aa15 biology/tabixpp: Undeprecate and update to 1.1.2 
Freebayes project did an about-face on using submodules, and now
defaults to external dependencies, so back to installing tabixpp
separately.

A few minor updates since 1.0.0.
Changes: https://github.com/vcflib/tabixpp/releases
 2025-02-18 09:39:35 -06:00
Jason W. Bacon
38e86db59c biology/tabixpp: Update to 1.1.2 
Undeprecate: Freebayes project did a about-face on using
submodules, and now defaults to external dependencies.
 2025-02-18 09:39:35 -06:00
Jason W. Bacon
4bbc358077 biology/vsearch: Update to 2.29.4 
Fix regression from 2.23.0 regarding chimera detection
Add pragma to ensure correct code
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout
 2025-02-16 08:21:06 -06:00
wen
a1ad8f94f1 biology/py-biopython: Update 1.83 => 1.85 
News:
https://github.com/biopython/biopython/blob/biopython-185/NEWS.rst

PR:		284780
Approved by:	Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer)
 2025-02-15 20:08:17 +03:00