a5a000df3b
lang/go: Change DEFAULT to 1.21
...
PR: 277776
Approved by: portmgr (exp-run)
2024-03-24 15:29:00 +01:00
eb44cf3c6f
biology/minimap2: Move man page to share/man
...
Approved by: portmgr (blanket)
2024-03-22 16:29:47 +09:00
97868be6ca
biology/prodigy-lig: update 1.0.1 → 1.1.0
...
Reported by: portscout
2024-03-21 03:08:33 -07:00
719334cd85
biology/bifrost: Update to 1.3.5
...
A few new features and bug fixes
Some important changes in CLI behavior
Changes: https://github.com/pmelsted/bifrost/releases
Reported by: portscout
2024-03-18 09:29:43 -05:00
43e4ca8d05
py-cutadapt: Update to 4.7
...
Send error message to stderr
Add support for single-ended uBAM
Drop Python 3.7
Changes: https://cutadapt.readthedocs.io/en/stable/changes.html
Reported by: portscout
2024-03-16 08:31:06 -05:00
59bdd5ade7
biology/minimap2: Update to 2.27
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Several new features and a few bug fixes
Changes: https://github.com/lh3/minimap2/releases
Reported by: portscout
2024-03-13 08:44:27 -05:00
509705557f
biology/seqkit: update 2.7.0 → 2.8.0
...
Reported by: portscout
2024-03-12 12:42:11 -07:00
1947368c6b
devel/grpc: Update to 1.62.0
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- Bump PORTREVISION of dependent ports for shlib change
Broken ports are skipped:
- science/py-tensorflow
- sysutils/apache-mesos
Changes: https://github.com/grpc/grpc/releases
2024-03-09 22:05:20 +08:00
ad0091716c
biology/taxonkit: update 0.15.1 → 0.16.0
...
Reported by: portscout
2024-03-08 14:34:42 -08:00
5b32e83eaa
biology/seqkit: update 2.6.1 → 2.7.0
...
Reported by: portscout
2024-03-08 14:34:42 -08:00
8d3eb5c77d
biology/py-pyrodigal: update 3.2.2 → 3.3.0
...
Reported by: portscout
2024-03-08 14:34:40 -08:00
b7ad936058
biology/ncbi-cxx-toolkit: update 28.0.0 → 28.0.2
...
Reported by: portscout
2024-03-08 02:25:49 -08:00
c779176e8a
biology/locarna: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-03 10:04:08 +00:00
dfc94f5f31
biology/abyss: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-03 10:04:08 +00:00
7990e83700
biology/vsearch: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:35:56 +00:00
5ebea8ee63
biology/viennarna: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:35:56 +00:00
ebba67d68e
biology/vcftools: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:35:56 +00:00
44f5f66eff
biology/vcflib: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:35:56 +00:00
0c132a2ef2
biology/vcf2hap: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:07:47 +00:00
0a569bfa8a
biology/vcf-split: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:04:57 +00:00
5c2b06d538
biology/treekin: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 20:02:27 +00:00
7552b0227f
biology/scrm: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:59:23 +00:00
01064ce0bd
biology/samtools: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:40:58 +00:00
3312d5f901
biology/peak-classifier: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:37:42 +00:00
f246c25371
biology/minimap2: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:29:26 +00:00
058e4213c9
biology/jellyfish: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:17:36 +00:00
b60356bd28
biology/generand: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:14:06 +00:00
b73c0ced99
biology/fastq-trim: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:08:45 +00:00
39013231fc
biology/fasda: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 19:03:05 +00:00
10b8d299f5
biology/biosig: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 18:49:11 +00:00
17190fc6cf
biology/biolibc-tools: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 18:44:44 +00:00
29f179ab37
biology/bcftools: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 18:38:43 +00:00
12b1194da2
biology/ad2vcf: Move man pages to share/man
...
Approved by: portmgr (blanket)
2024-03-02 18:32:34 +00:00
5d4139f8bd
devel/py-setuptools-scm: update to 8.0.4
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Directory and PORTNAME changed to match normalised name in release
tarball; consumers updated to match.
Although setuptools itself is specified as a run dependency in the
Python package metadata, it is currently left out here to prevent
environment pollution until at least PR 270510 is committed.
Additionally, this version of setuptools-scm requires setuptools>=61,
which means this version is only meant for USE_PYTHON=pep517 ports
as all USE_PYTHON=distutils ports will switch to devel/py-setuptools58
also after PR 270510. science/py-emmet-core is switched to
devel/py-setuptools_scm7 accordingly, as it specifies setuptools-scm<8.
devel/py-{flit-scm,hatch-vcs} have ${PY_SETUPTOOLS} added to
RUN_DEPENDS to compensate.
Further details: https://wiki.freebsd.org/Python/setuptools
Reported by: yuri
Co-authored by: matthew
Exp-run by: antoine (earlier iteration)
Approved by: yuri (science/py-emmet-core, previous iteration)
PR: 272134
Differential Revision: https://reviews.freebsd.org/D39288
2024-02-29 02:18:32 -05:00
ddb11fbe97
biology/py-macs3: Update to 3.0.1
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Minor bug fix release
Changes: https://github.com/macs3-project/MACS/releases
2024-02-28 07:29:15 -06:00
1b6126c582
biology/pooler: Moved man to share/man
...
Approved by: portmgr (blanket)
2024-02-22 14:23:50 +01:00
f5db6921ff
biology/mafft: Moved man to share/man
...
Approved by: portmgr (blanket)
2024-02-22 14:23:49 +01:00
3263fab7c9
biology/iolib: Moved man to share/man
...
Approved by: portmgr (blanket)
2024-02-22 14:23:48 +01:00
806984bb1b
biology/infernal: Moved man to share/man
...
Approved by: portmgr (blanket)
2024-02-22 14:23:47 +01:00
c0800517ea
biology/hmmer: Moved man to share/man
...
Approved by: portmgr (blanket)
2024-02-22 14:23:46 +01:00
2044d70d1f
biology/exonerate: Moved man to share/man
...
Approved by: portmgr (blanket)
2024-02-22 14:23:45 +01:00
917c3f128b
devel/grpc: Update to 1.61.1
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- Bump PORTREVISION of dependent ports for shlib change
Changes: https://github.com/grpc/grpc/releases
2024-02-21 23:06:22 +08:00
2ad82a1068
*/*: Replace format=bsdtar with format=ustar in tar archive operations
...
... because the undocumented format bsdtar adds paxheaders on
some systems, therefore breaking the fetch.
The documentation for format=bsdtar should be added:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=277139
Approved by: portmgr (blanket unbreak)
2024-02-18 17:48:08 -08:00
9eba6162f8
*/*: bump PORTREVISION after OpenMPI upgrade
2024-02-18 10:29:31 +01:00
306ace3962
biology/biostar-tools: Update to 1.10.1_3
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Add sra-tools to metaport deps on aarch64
Clean up pkg-desc
2024-02-16 07:42:11 -06:00
db616534ff
devel/boost: bump consumers after library update
2024-02-13 17:44:22 +03:00
3fad843b18
biology/py-bx-python: update 0.10.0 → 0.11.0
...
Reported by: portscout
2024-02-12 15:07:35 -08:00
7e5aa2085f
all: Bump PORTREVISION after lang/go* update
...
PR: 276530
2024-02-11 10:39:17 +00:00
7c280eb424
biology/py-cutadapt: Update to 4.6
...
Numerous bug fixes and enhancements since 3.3
Changes: https://github.com/marcelm/cutadapt/tags
PR: 276814
Reported by: wen
2024-02-06 06:55:32 -06:00
e35d3c95a0
biology/py-dnaio: Update to 1.2.0
...
Numerous bug fixes and enhancements since 0.5.1
Changes: https://github.com/marcelm/dnaio/tags
PR: 276814
Reported by: wen
2024-02-06 06:51:39 -06:00
Muhammad Moinur Rahman
Yasuhiro Kimura
Yuri Victorovich
Jason W. Bacon
Po-Chuan Hsieh
Nuno Teixeira
Charlie Li
Thierry Thomas
Dima Panov
Ashish SHUKLA