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3750 commits

Author SHA1 Message Date
Ashish SHUKLA
1a5ede5f36
all: Bump PORTREVISION after lang/go* update 
PR:		274405
(cherry picked from commit 0505b712df)
 2023-12-07 15:06:56 +00:00
Po-Chuan Hsieh
df6a298fb0
biology/rubygem-bio: Update to 2.0.5 
Changes:	https://github.com/bioruby/bioruby/blob/master/RELEASE_NOTES.rdoc
 2023-09-30 08:46:30 +08:00
Po-Chuan Hsieh
4c14d7a290
biology/libsbml: Update to 5.20.2 
Changes:	https://github.com/sbmlteam/libsbml/releases
 2023-09-30 08:44:19 +08:00
Jason W. Bacon
f3576d9ad8 biology/wfa2-lib: Update to 2.3.4 
A few bug fixes
Changes: https://github.com/smarco/WFA2-lib/releases

Reported by:    portscout
 2023-09-29 13:24:07 -05:00
Muhammad Moinur Rahman
db3d647fde biology/mothur: Remove CC/CPP/CXX exports 
USES=llvm now by default exports CC/CPP/CXX so remove those
Approved by:	portmgr (blanket)
 2023-09-28 20:56:25 +02:00
Dima Panov
21d8008e86
devel/boost*: bump all consumers after 1.83.0 2023-09-27 17:36:30 +03:00
Thierry Thomas
a0ed0dce34 /*: bump PORTREVISION after the upgrade of SuiteSparse 2023-09-20 19:57:40 +02:00
Yuri Victorovich
3f1d9aaddd biology/kmcp: update 0.9.3 → 0.9.4 
Reported by:	portscout
 2023-09-17 23:27:25 -07:00
Yuri Victorovich
aa82e618e4 biology/seqan3: update 3.2.0 → 3.3.0 
PR:		273670
Reported by:	 Lorenzo Salvadore <salvadore@freebsd.org>
 2023-09-10 11:10:47 -07:00
Jason W. Bacon
8abd028788 biology/pooler: Update to 1.88 
Fix infinite loop

Changes: https://ssb22.user.srcf.net/pooler/#changes

PR:             273604
Reported by:    silas-freebsd@flatline.org.uk
 2023-09-10 08:06:18 -05:00
Dmitri Goutnik
8e4bc57934 all: Bump PORTREVISION after lang/go* update 2023-09-08 09:34:56 -05:00
Po-Chuan Hsieh
1d86601d32
biology/peak-classifier: Clean up USES=python 
Approved by:	portmgr (blanket)
With hat:	python
 2023-09-07 04:50:36 +08:00
Joseph Mingrone
5d6c87d761
biology/hyphy: Update to 2.5.53 
Changes:	https://github.com/veg/hyphy/releases/tag/2.5.53
Sponsored by:	The FreeBSD Foundation
 2023-09-05 11:49:35 -03:00
Joseph Mingrone
8a1ec0de6b
biology/iqtree: Update to 2.2.2.7 
Changes:	https://github.com/iqtree/iqtree2/releases/tag/v2.2.2.7
Sponsored by:	The FreeBSD Foundation
 2023-09-04 23:45:37 -03:00
Yuri Victorovich
e06be01f1e biology/spoa: update 4.0.7 → 4.1.0 
Reported by:	portscout
 2023-08-29 09:59:01 -07:00
Yuri Victorovich
c776c74fb1 biology/bioparser: update 3.0.15 → 3.1.0 
Reported by:	portscout
 2023-08-29 00:32:45 -07:00
Yuri Victorovich
5bc123b587 biology/biosoup: Install cmake files 2023-08-29 00:32:45 -07:00
Yuri Victorovich
f97472faf9 biology/py-resdk: update 19.0.0 → 19.0.1 
Reported by:	portscout
 2023-08-27 23:31:28 -07:00
Jason W. Bacon
6a07479763 biology/ncbi-blast+: Update to 2.14.1 
A few minor fixes and enhancements
Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/

Reported by:    portscout
 2023-08-26 07:57:04 -05:00
Yuri Victorovich
498d092add biology/seqwish: Add comment 2023-08-24 23:22:32 -07:00
Yuri Victorovich
61ea32a58c biology/py-resdk: update 18.0.0 → 19.0.0 
Reported by:	portscout
 2023-08-24 20:24:38 -07:00
Yuri Victorovich
8b368b8263 biology/taxonkit: Update 0.14.2 → 0.15.0 
Reported by:	portscout
 2023-08-22 12:20:56 -07:00
Yuri Victorovich
37b580d92e biology/mashmap: Update 3.1.0 → 3.1.1 2023-08-22 09:32:45 -07:00
Yuri Victorovich
6eba0e19d7 biology/mashmap: Update 3.0.6 → 3.1.0 
Reported by:	portscout
 2023-08-21 23:55:32 -07:00
Jason W. Bacon
0e8f22496e biology/star: Fix SIMD issue on non-amd64 
Also remove some extraneous build flags from upstream Makefile

PR:             273240
Reported by:    dizzy
 2023-08-21 09:33:20 -05:00
Ganael LAPLANCHE
22e222cbce devel/onetbb: Update to 2021.10.0 
and bump dependent ports' revisions.

Release notes: https://github.com/oneapi-src/oneTBB/releases/tag/v2021.10.0
 2023-08-21 12:09:23 +02:00
Piotr Kubaj
9f36518602 biology/star: fix build on !amd64 
The port tries to force AVX2, but it's only available on amd64.
 2023-08-19 21:51:47 +00:00
Muhammad Moinur Rahman
4b87c88e29 biology/viennarna: Mark BROKEN on 14 
Fails to compile with:
error: no member named 'bind2nd' in namespace 'std'

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
 2023-08-18 08:57:13 +02:00
Muhammad Moinur Rahman
bb82d0e6e1 biology/lamarc: Mark BROKEN on 14 
Fails to compile with:
error: no matching function for call to 'make_pair'

Sponsored by:	The FreeBSD Foundation
 2023-08-18 08:57:13 +02:00
Muhammad Moinur Rahman
a5b5a22ade biology/mothur: Fix build on 14 
Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
 2023-08-18 08:57:12 +02:00
Jason W. Bacon
a382bcefaf biology/star: Update to 2.7.11a 
A few bug fixes and new features
Add USE_GCC as a temporary hack for input read issue
This was also an issue in 2.7.10b

Changes: https://github.com/alexdobin/STAR/releases
 2023-08-17 11:01:09 -05:00
Yuri Victorovich
219d517c10 biology/seqwish: Broken on i386 
Reported by:	fallout
 2023-08-16 22:27:09 -07:00
Yuri Victorovich
ec80eff163 biology/mothur: Fix build with clang-16 
Reported by:	fallout
 2023-08-15 00:42:10 -07:00
Jason W. Bacon
f38473fec0 biology/bifrost: Control -march via CPUTYPE make variable 
Also disable hard-coded -O3 in cmake to respect user env

PR:             272651
Reported by:    yuri
Reviewed by:    nimaje+fbz@bureaucracy.de, dizzy
 2023-08-12 09:38:47 -05:00
Piotr Kubaj
6c5416c589 biology/cd-hit: allow to build without GCC on libomp-less systems 2023-08-12 03:37:47 +02:00
Jason W. Bacon
9b09bd9028 biology/peak-classifier: Update to 0.1.4.11 
Updates for biolibc GFF3 API changes
 2023-08-11 15:44:14 -05:00
Jason W. Bacon
e9b6ad4f59 biology/biolibc-tools: Update to 0.1.4.9 
Update for biolibc GFF3 API changes
 2023-08-11 15:40:49 -05:00
Jason W. Bacon
67773b0db3 biology/fasda: Update to 0.1.4 
Add --debug
Replace --map-gene with --feature-type for more flexibility
Use extended REs for gff3 feature selection (default = RNA$|transcript$|gene_segment$, same as transcript in GTF)
Add --output-dir
Support |-separated ID aliases (report last alias)
Support outsourcing abundance calculation (default = stringtie)
Several bug fixes and minor enhancements

Changes: https://github.com/auerlab/fasda/releases
 2023-08-11 15:39:06 -05:00
Jason W. Bacon
c978aad1b0 biology/biolibc: Update to 0.2.5 
Make header files C++ compatible (extern C)
bl_chrom_name_cmp(): Support names with embedded digits, e.g. chr2p
bl_gff_extract_attribute(): Improve performance
gff -> gff3 to distinguish from past and future GFF specs
Silence some compiler warnings

Changes: https://github.com/auerlab/biolibc/releases
 2023-08-11 15:35:11 -05:00
Jason W. Bacon
0f2f80ca38 biology/sra-tools: Update to 3.0.6 
Major code and build system rework since 2.11
Now supports aarch64, unblocking rna-seq and atac-seq metaports
Changes: https://github.com/ncbi/sra-tools/commits/master

Reported by:    portscout
 2023-08-10 12:17:24 -05:00
Joseph Mingrone
8d0b7976cd
biology/hyphy: Update to 2.5.52 
- FEL test is now passing, so remove comment about it failing.
- Remove armv7 support since most tests are segfaulting.

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.52
Sponsored by:	The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D41393
Tested by:	fuz (armv7)
 2023-08-09 14:39:17 -03:00
Yuri Victorovich
9f724a0f69 biology/seqkit: Update 2.5.0 → 2.5.1 
Reported by:	portscout
 2023-08-08 22:52:28 -07:00
Muhammad Moinur Rahman
6d558714df biology/seqan-apps: Fix build with llvm16 
Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
 2023-08-06 23:53:04 +02:00
Muhammad Moinur Rahman
46e066a42e biology/augustus: Fix build with llvm16 
Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
 2023-08-06 23:53:03 +02:00
Jason W. Bacon
e97c345748 biology/py-macs2: Update to 2.2.9.1 
Mainly updates to dependencies
Changes: https://github.com/macs3-project/MACS/releases
Added test target

Reported by:    portscout
 2023-08-06 13:17:52 -05:00
Jason W. Bacon
322706681c p5-transdecoder: Update to 5.7.1 
A few general fixes, mostly updates for Docker

Reported by:    portscout
 2023-08-05 15:58:40 -05:00
Muhammad Moinur Rahman
1708933a86 biology/p5-TrimGalore: Fix build 
LICENSE had a typo.

Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
 2023-08-05 22:05:05 +02:00
Muhammad Moinur Rahman
16f82a503a biology/primer3: Fix build with llvm16 
Approved by:	portmgr (blanket)
Sponsored by:	The FreeBSD Foundation
 2023-08-05 20:55:50 +02:00
Jason W. Bacon
fa7be670b4 biology/py-htseq: Update to 2.0.4 
Mainly improved warnings
Changes: https://github.com/htseq/htseq

Reported by:    portscout
 2023-08-05 11:40:26 -05:00
Jason W. Bacon
a084c0b088 biology/py-multiqc: Update to 1.15 
Major performance boost for file search
New "Librarian" module
Numerous enhancements and module updates
Changes: https://github.com/ewels/MultiQC/releases

Reported by:    portscout
 2023-08-05 11:18:37 -05:00