summaryrefslogtreecommitdiff
path: root/biology
AgeCommit message (Collapse)Author
2024-06-15all: Bump after lang/go121 updateAshish SHUKLA
MFH: 2024Q2 (cherry picked from commit 746fa696a12ef1ca798e36baf087f579375b8cd1)
2024-05-13all: Bump after lang/go121 updateAshish SHUKLA
MFH: 2024Q2 (cherry picked from commit fce0cc32720e61042bc675152b116f9e61532e92)
2024-04-28biology/spoa: Broken on i386Yuri Victorovich
Reported by: fallout (cherry picked from commit b9636819d752a4b79a93af276df3d44c96ea6709)
2024-04-15all: Bump after lang/go121 updateAshish SHUKLA
MFH: 2024Q2 (cherry picked from commit 32b284679a1954ef1e0c0d52c4741d00e36dc6e0)
2024-04-12biology/migrate: Use system zlib instead of excluding it from extractNuno Teixeira
Fixes: dc29da5db6e6e: Fix extract on aarch64 (cherry picked from commit 882ecb2d7f689fa041a90196eff83985891af398)
2024-04-12biology/migrate: Fix distinfoNuno Teixeira
Upstream re-rolled tarball. (cherry picked from commit 42af8b83722f85e725aa0450d8557c8a5d4a742b)
2024-04-08biology/py-biopython: Update to 1.83Wen Heping
PR: 277979 Reported by: wen@ Approved by: maintainer
2024-04-05biology/py-scikit-bio: update 0.5.9 → 0.6.0Yuri Victorovich
Reported by: portscout
2024-04-05biology/py-resdk: update 20.0.0 → 21.1.0Yuri Victorovich
Reported by: portscout
2024-04-05biology/{,py-}biosig: update 2.5.2 → 2.6.0Yuri Victorovich
Reported by: portscout
2024-04-05biology/trimmomatic: Release to ports@Jason W. Bacon
Focusing on fastq-trim from now on.
2024-04-05biology/p5-TrimGalore: Release to ports@Jason W. Bacon
Focusing on fastq-trim from now on.
2024-04-05biology/py-cutadapt: Release to ports@Jason W. Bacon
Focusing on fastq-trim from now on
2024-04-05biology/peak-classifier: Clean up USES=pythonPo-Chuan Hsieh
- Fix d6b521a455883ea2b387fb9cf61637ea879b746c - Reapply 1d86601d3200c531e7fcd174cdd1feaf6d616518 USES=python means USES=python:3.8+ now. Approved by: portmgr (blanket) With hat: python
2024-04-04biology/pbseqan: Set EXPIRATION_DATEMuhammad Moinur Rahman
- Has been marked DEPRECATED for around 5 years - Use biology/seqan - Set EXPIRATION_DATE 2024-05-05
2024-04-04biology/btllib: update 1.7.0 → 1.7.1Yuri Victorovich
Reported by: portscout
2024-04-03biology/ncbi-cxx-toolkit: update 28.0.2 → 28.0.3Yuri Victorovich
Reported by: portscout
2024-03-31biology/migrate: Update to 5.0.6Nuno Teixeira
ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY
2024-03-27biology/migrate: Fix extractNuno Teixeira
Extract fails on aarch64 with error: (sample) "dynsections.js: Cannot restore extended attributes: com.apple.quarantine com.apple.quarantine: No such file or directory" tar: Error exit delayed from previous errors.- Fix extract with: --no-same-owner --no-same-permissions
2024-03-27biology/migrate: Update to 5.0.5Nuno Teixeira
- Switch to DISTVERSION - Add license - Pet portlint, portclippy and portfmt - Take maintainership ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY
2024-03-24lang/go: Change DEFAULT to 1.21Muhammad Moinur Rahman
PR: 277776 Approved by: portmgr (exp-run)
2024-03-22biology/minimap2: Move man page to share/manYasuhiro Kimura
Approved by: portmgr (blanket)
2024-03-21biology/prodigy-lig: update 1.0.1 → 1.1.0Yuri Victorovich
Reported by: portscout
2024-03-18biology/bifrost: Update to 1.3.5Jason W. Bacon
A few new features and bug fixes Some important changes in CLI behavior Changes: https://github.com/pmelsted/bifrost/releases Reported by: portscout
2024-03-16py-cutadapt: Update to 4.7Jason W. Bacon
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
2024-03-13biology/minimap2: Update to 2.27Jason W. Bacon
Several new features and a few bug fixes Changes: https://github.com/lh3/minimap2/releases Reported by: portscout
2024-03-12biology/seqkit: update 2.7.0 → 2.8.0Yuri Victorovich
Reported by: portscout
2024-03-09devel/grpc: Update to 1.62.0Po-Chuan Hsieh
- 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
2024-03-08biology/taxonkit: update 0.15.1 → 0.16.0Yuri Victorovich
Reported by: portscout
2024-03-08biology/seqkit: update 2.6.1 → 2.7.0Yuri Victorovich
Reported by: portscout
2024-03-08biology/py-pyrodigal: update 3.2.2 → 3.3.0Yuri Victorovich
Reported by: portscout
2024-03-08biology/ncbi-cxx-toolkit: update 28.0.0 → 28.0.2Yuri Victorovich
Reported by: portscout
2024-03-03biology/locarna: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-03biology/abyss: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/vsearch: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/viennarna: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/vcftools: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/vcflib: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/vcf2hap: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/vcf-split: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/treekin: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/scrm: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/samtools: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/peak-classifier: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/minimap2: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/jellyfish: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/generand: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/fastq-trim: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/fasda: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
2024-03-02biology/biosig: Move man pages to share/manNuno Teixeira
Approved by: portmgr (blanket)
generated by cgit v1.2.3 (git 2.25.1) at 2025-01-18 12:08:48 +0000