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* biology/pooler: Moved man to share/manMuhammad Moinur Rahman2024-02-221-1/+5
| | | | Approved by: portmgr (blanket)
* biology/mafft: Moved man to share/manMuhammad Moinur Rahman2024-02-223-3/+4
| | | | Approved by: portmgr (blanket)
* biology/iolib: Moved man to share/manMuhammad Moinur Rahman2024-02-222-24/+26
| | | | Approved by: portmgr (blanket)
* biology/infernal: Moved man to share/manMuhammad Moinur Rahman2024-02-222-11/+13
| | | | Approved by: portmgr (blanket)
* biology/hmmer: Moved man to share/manMuhammad Moinur Rahman2024-02-222-21/+23
| | | | Approved by: portmgr (blanket)
* biology/exonerate: Moved man to share/manMuhammad Moinur Rahman2024-02-222-4/+6
| | | | Approved by: portmgr (blanket)
* devel/grpc: Update to 1.61.1Po-Chuan Hsieh2024-02-211-1/+1
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
* */*: Replace format=bsdtar with format=ustar in tar archive operationsYuri Victorovich2024-02-191-1/+1
| | | | | | | | | | ... 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)
* */*: bump PORTREVISION after OpenMPI upgradeThierry Thomas2024-02-181-1/+1
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* biology/biostar-tools: Update to 1.10.1_3Jason W. Bacon2024-02-163-15/+18
| | | | | Add sra-tools to metaport deps on aarch64 Clean up pkg-desc
* devel/boost: bump consumers after library updateDima Panov2024-02-134-4/+4
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* biology/py-bx-python: update 0.10.0 → 0.11.0Yuri Victorovich2024-02-122-4/+4
| | | | Reported by: portscout
* all: Bump PORTREVISION after lang/go* updateAshish SHUKLA2024-02-115-4/+5
| | | | PR: 276530
* biology/py-cutadapt: Update to 4.6Jason W. Bacon2024-02-062-7/+6
| | | | | | | | Numerous bug fixes and enhancements since 3.3 Changes: https://github.com/marcelm/cutadapt/tags PR: 276814 Reported by: wen
* biology/py-dnaio: Update to 1.2.0Jason W. Bacon2024-02-062-6/+7
| | | | | | | | Numerous bug fixes and enhancements since 0.5.1 Changes: https://github.com/marcelm/dnaio/tags PR: 276814 Reported by: wen
* biology/diamond: Update to 2.1.9Joseph Mingrone2024-02-043-19/+4
| | | | | Changelog: https://github.com/bbuchfink/diamond/releases/tag/v2.1.9 Sponsored by: The FreeBSD Foundation
* biology/metaeuk: Broken on powerpc64leYuri Victorovich2024-02-041-0/+1
| | | | Reported by: fallout
* biology/hhsuite: Fix build on some systems by adding missing C++ #include ↵Yuri Victorovich2024-02-041-0/+12
| | | | | | statement Reported by: fallout
* biology/python-nexus: Update to 2.9.0 and fix build with python-3.11Wen Heping2024-02-033-25/+9
| | | | PR: 275494
* biology/py-newick: Add new portWen Heping2024-02-034-0/+22
| | | | A python module to read and write the Newick format.
* biology/ngs-sdk: Not for powerpc, powerpc64leYuri Victorovich2024-02-021-2/+2
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* biology/py-bx-python: update to 0.10.0Ruslan Makhmatkhanov2024-01-282-5/+4
| | | | | | | | | | Update to 0.10.0. This release adds support for python 3.11 Changes: https://github.com/bxlab/bx-python/releases/tag/v0.10.0 PR: 276683 PR: 275494 Approved by: yuri (maintainer)
* */*: bump PORTREVISION after the upgrade to SuiteSparseThierry Thomas2024-01-282-2/+2
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* biology/htslib: Moved man to share/manMuhammad Moinur Rahman2024-01-272-7/+9
| | | | Approved by: portmgr (blanket)
* biology/biolibc: Impelled to share/manMuhammad Moinur Rahman2024-01-232-472/+475
| | | | Approved by: portmgr (blanket)
* biology/vsearch: Update to 2.27.0Jason W. Bacon2024-01-232-4/+4
| | | | | | | Add FASTQ support to usearch_global and search_exact Code cleanup and manual clarifications Reported by: portscout
* biology/py-pyrodigal: update 3.2.1 → 3.2.2Yuri Victorovich2024-01-212-4/+4
| | | | Reported by: portscout
* biology/py-htseq: Fix build with python-3.11Wen Heping2024-01-211-2/+2
| | | | | PR: 275494 Approved by: portmgr@(blanket, fix build)
* biology/ncbi-cxx-toolkit: Broken on armv7Yuri Victorovich2024-01-211-0/+1
| | | | Reported by: fallout
* biology/py-mrcfile: update 1.4.3 → 1.5.0Yuri Victorovich2024-01-202-5/+4
| | | | Reported by: portscout
* biology/bowtie2: Update to 2.5.3Jason W. Bacon2024-01-182-4/+4
| | | | | | | A few bug fixes Add option for faster indexing of small indexes Reported by: portscout
* biology/recombine: Remove expired portRene Ladan2024-01-186-268/+0
| | | | 2024-01-17 biology/recombine: Upstream advises to use biology/lamarc
* biology/seqio: Remove expired portMuhammad Moinur Rahman2024-01-188-354/+0
| | | | 2024-01-17 biology/seqio: Upstream last release was in 2000
* biology/sim4: Remove expired portMuhammad Moinur Rahman2024-01-184-40/+0
| | | | 2024-01-17 biology/sim4: Upstream last update was in 2005
* biology/metaeuk: fix build on powerpc64le by disabling openmp until libomp ↵Piotr Kubaj2024-01-161-2/+3
| | | | is fixed
* */*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0Thierry Thomas2024-01-132-2/+2
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* biology/mashmap: Broken on armv7Yuri Victorovich2024-01-131-0/+1
| | | | Reported by: https://portsfallout.com/
* MANPREFIX: eliminate its usageBaptiste Daroussin2024-01-125-50/+51
| | | | While here move manpages to share/man
* biology/metaeuk: Add to NOT_FOR_ARCHS, and correct BROKENxx linesYuri Victorovich2024-01-121-1/+2
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* biology/metaeuk: Correct the reason in the BROKEN_xx lineYuri Victorovich2024-01-121-1/+1
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* biology/metaeuk: Not for 32-bit architecturesYuri Victorovich2024-01-121-2/+1
| | | | metaeuk produces wrong results there.
* biology/metaeuk: Broken on i386, armv7, powerpc64Yuri Victorovich2024-01-121-0/+4
| | | | Reported by: https://portsfallout.com/
* biology/btllib: Temporarily not for non-64-bit architecturesYuri Victorovich2024-01-121-0/+2
| | | | | | Until the breakage is fixed by the upstream. Reported by: https://portsfallout.com/
* biology/atac-seq: Update to 0.2.0Jason W. Bacon2024-01-102-2/+8
| | | | Add biology/py-macs3 dep to metaport
* biology/py-macs3: Peak caller for TF binding sitesJason W. Bacon2024-01-108-0/+104
| | | | | | | | | MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying transcription factor (TF) binding sites. Such sites are generated by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq (Assay for Transposase Accessible Chromatin Sequencing). MACS identifies "peaks" in the genome sequence, which are areas enriched in bound TFs or accessible chromatin.
* MAN?PREFIX: eleminate its usage and move man to share/manBaptiste Daroussin2024-01-105-33/+32
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* MAN[1-5]PREFIX: eleminate its usage and move man to share/manBaptiste Daroussin2024-01-094-22/+24
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* biology/mashmap: update 3.1.2 → 3.1.3Yuri Victorovich2024-01-052-5/+8
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* biology/ncbi-cxx-toolkit: update 27.0.0 → 28.0.0Yuri Victorovich2024-01-053-17/+6
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* */*: chase the upgrade of BLAS / LAPACK to 3.12.0Thierry Thomas2024-01-012-1/+2
| | | | PR: 275860
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