| .. |
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abyss
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biology/abyss: update 2.3.8 → 2.3.9
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2024-09-12 02:18:11 -07:00 |
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ad2vcf
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biology/ad2vcf: Update to 0.1.6.19
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2024-05-19 08:41:41 -05:00 |
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andi
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biology/andi: New ports: Efficient estimation of evolutionary distances
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2024-09-07 14:31:10 -07:00 |
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artemis
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atac-seq
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biology/atac-seq: Update to 0.2.0
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2024-01-10 10:05:41 -06:00 |
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augustus
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*/*: chase SuiteSparse’s upgrade
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2024-04-29 22:08:56 +02:00 |
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avida
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*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
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2023-12-31 01:37:05 +01:00 |
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babel
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biology/babel: Update WWW
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2023-10-30 23:37:03 +01:00 |
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bamtools
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*/*: Bump dependencioes after devel/jsoncpp update
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2024-09-12 09:20:06 -07:00 |
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bamutil
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barrnap
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biology/barrnap: Update descr
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2022-11-24 19:12:18 -08:00 |
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bbmap
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bcf-score
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biology/bcf-score: Unbreak build with clang 16
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2023-07-16 08:19:06 -05:00 |
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bcftools
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biology/bcftools: Move man pages to share/man
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2024-03-02 18:38:43 +00:00 |
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bedtools
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biology/bedtools: Update to 2.31.1
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2023-11-08 10:42:09 -06:00 |
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bfc
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bifrost
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biology/bifrost: Update to 1.3.5
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2024-03-18 09:29:43 -05:00 |
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bio-mocha
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biology/bio-mocha: Update to 1.16
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2023-01-05 17:21:03 -06:00 |
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bioawk
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biococoa
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audio/opus: bump consumers after update to 1.4
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2023-04-25 17:17:15 +02:00 |
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biolibc
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biology/biolibc: Update to 0.2.6.4
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2024-05-19 08:40:24 -05:00 |
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biolibc-tools
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biology/biolibc-tools: Move man pages to share/man
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2024-03-02 18:44:44 +00:00 |
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bioparser
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biology/bioparser: update 3.0.15 → 3.1.0
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2023-08-29 00:32:45 -07:00 |
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biosig
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biology/{.py-}biosig: update 2.6.0 → 2.6.1
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2024-08-05 07:37:01 -07:00 |
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biosoup
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biology/biosoup: Install cmake files
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2023-08-29 00:32:45 -07:00 |
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biostar-tools
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biology/biostar-tools: Update to 1.11
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2024-06-03 06:38:30 -05:00 |
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bolt-lmm
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*/*: Bump PORTVERSION of math/nlopt consumers
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2024-08-25 15:33:16 +02:00 |
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bowtie
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*/*: Update WWW to use HTTPS for sourceforge.net projects
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2023-11-06 11:03:47 +01:00 |
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bowtie2
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biology/bowtie2: Update to 2.5.4
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2024-05-24 06:33:53 -05:00 |
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btllib
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biology/btllib: update 1.7.2 → 1.7.3
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2024-07-27 13:19:18 -07:00 |
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bwa
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MAN?PREFIX: eleminate its usage and move man to share/man
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2024-01-10 09:16:01 +01:00 |
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canu
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biology/canu: Fix build with llvm16
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2023-07-20 19:42:34 +02:00 |
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cd-hit
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biology/cd-hit: allow to build without GCC on libomp-less systems
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2023-08-12 03:37:47 +02:00 |
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cdbfasta
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biology/cdbfasta: Update to 2023.07.10
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2023-07-11 10:40:27 -05:00 |
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checkm
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biology/checkm: update 1.2.0 → 1.2.2
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2024-04-23 01:40:35 -07:00 |
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chip-seq
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biology/chip-seq: Metaport for ChIP-Seq analysis
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2023-06-14 16:23:37 -05:00 |
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clustal-omega
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clustalw
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biology/clustalw: Unbreak build for clang 16
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2023-07-15 18:18:42 -05:00 |
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cufflinks
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devel/boost: bump consumers after library update
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2024-02-13 17:44:22 +03:00 |
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cytoscape
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biology/cytoscape: Broken on i386
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2024-05-25 18:45:24 -07:00 |
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ddocent
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*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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diamond
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biology/diamond: Update to 2.1.9
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2024-02-04 15:41:51 -04:00 |
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dsr-pdb
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devel/boost: bump consumers after library update
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2024-02-13 17:44:22 +03:00 |
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edlib
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emboss
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*/*: Refactor with IGNORE_WITH_MYSQL
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2023-12-29 19:24:39 +01:00 |
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erminej
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exonerate
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biology/exonerate: Moved man to share/man
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2024-02-22 14:23:45 +01:00 |
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fasda
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biology/fasda: Move man pages to share/man
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2024-03-02 19:03:05 +00:00 |
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fasta
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MAN[1-5]PREFIX: eleminate its usage and move man to share/man
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2024-01-09 16:41:04 +01:00 |
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fasta3
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MAN?PREFIX: eleminate its usage and move man to share/man
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2024-01-10 09:16:01 +01:00 |
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fastahack
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fastdnaml
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fastool
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fastp
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biology/fastp: Update to 0.23.4
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2023-05-31 10:40:00 -05:00 |
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fastq-trim
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biology/fastq-trim: Move man pages to share/man
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2024-03-02 19:08:45 +00:00 |
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fastqc
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biology/fastqc: Update to 0.12.1
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2023-03-04 18:17:20 -06:00 |
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fasttree
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fastx-toolkit
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biology/fastx-toolkit: Unbreak build on 14-CURRENT
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2023-03-07 11:28:13 -06:00 |
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fermi-lite
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biology/fermi-lite: fix build on powerpc64le
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2024-08-13 11:40:45 +02:00 |
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figtree
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flash
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fluctuate
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freebayes
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biology/freebayes: Drop redundant tabixpp dep
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2023-01-22 10:42:34 -06:00 |
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garlic
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gatk
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biology/gatk: Update COMMENT
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2024-08-04 13:13:15 -07:00 |
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gcta
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biology/gcta: Unbreak fetch
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2024-07-08 17:04:44 -05:00 |
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gemma
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*/*: bump PORTREVISION after the upgrade to OpenBLAS
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2024-06-21 19:49:24 +02:00 |
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generand
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biology/generand: Move man pages to share/man
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2024-03-02 19:14:06 +00:00 |
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gff2ps
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biology/gff2ps: drop maintainership
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2023-05-21 16:20:36 +00:00 |
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gffread
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gkl
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biology/gkl: New port: Accelerated kernel library for genomics
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2024-08-04 13:09:41 -07:00 |
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gmap
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gperiodic
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accessibility/at-spi2-core: update to 2.46.0
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2023-03-02 06:23:10 +01:00 |
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graphlan
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groopm
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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haplohseq
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devel/boost: bump consumers after library update
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2024-02-13 17:44:22 +03:00 |
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hhsuite
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*/*: bump PORTREVISION after OpenMPI upgrade
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2024-02-18 10:29:31 +01:00 |
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hisat2
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hmmer
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biology/hmmer: Moved man to share/man
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2024-02-22 14:23:46 +01:00 |
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htslib
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biology/htslib: Moved man to share/man
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2024-01-27 13:37:30 +01:00 |
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hyphy
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biology/hyphy: Update to 2.5.62
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2024-06-21 13:58:09 -03:00 |
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igv
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audio/opus: bump consumers after update to 1.4
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2023-04-25 17:17:15 +02:00 |
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infernal
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biology/infernal: Moved man to share/man
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2024-02-22 14:23:47 +01:00 |
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iolib
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biology/iolib: Moved man to share/man
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2024-02-22 14:23:48 +01:00 |
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iqtree
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biology/iqtree: Update to 2.3.6
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2024-09-07 22:53:14 -03:00 |
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jalview
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biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1
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2023-06-18 02:58:53 -07:00 |
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jellyfish
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biology/jellyfish: Move man pages to share/man
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2024-03-02 19:17:36 +00:00 |
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kallisto
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biology/kallisto: Update to 0.51.0,1
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2024-07-27 07:02:57 -05:00 |
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kmcp
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all: Bump after lang/go121 update
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2024-08-09 06:24:08 +00:00 |
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lamarc
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biology/lamarc: Mark BROKEN on 14
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2023-08-18 08:57:13 +02:00 |
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libbigwig
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biology/libbigwig: Fix name-clashing in roundup
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2023-12-28 18:03:34 -05:00 |
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libcombine
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biology/libcombine: Fix build with libsbml 5.20.0
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2023-05-27 12:24:05 +08:00 |
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libgff
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libgtextutils
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libneurosim
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devel/automake: Update to 1.17
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2024-07-20 13:27:02 +02:00 |
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libnuml
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libsbml
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biology/libsbml: Update to 5.20.4
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2024-09-09 02:36:57 +08:00 |
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libsedml
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biology/libsedml: Fix build with libsbml 5.20.0
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2023-05-27 12:24:05 +08:00 |
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linux-foldingathome
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biology/linux-foldingathome: Point MASTER_SITES to the new location
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2024-08-12 14:58:05 +02:00 |
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locarna
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biology/locarna: Move man pages to share/man
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2024-03-03 10:04:08 +00:00 |
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mafft
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biology/mafft: Moved man to share/man
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2024-02-22 14:23:49 +01:00 |
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mapm3
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mashmap
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biology/mashmap: Broken on armv7
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2024-01-12 17:57:41 -08:00 |
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megahit
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biology/megahit: Add cmake patch to respect ports build flags
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2022-11-24 08:10:13 -06:00 |
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metaeuk
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biology/metaeuk: update 6 → 7
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2024-06-01 01:10:52 -07:00 |
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migrate
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biology/migrate: fix build on !x86
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2024-07-09 12:04:31 +02:00 |
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minimap2
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biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors
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2024-07-20 14:55:08 -05:00 |
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mmseqs2
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molden
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*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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mothur
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biology/mothur: update 1.48.0 → 1.48.1
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2024-05-16 01:56:44 -07:00 |
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mrbayes
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mummer
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*/*: Update WWW to use HTTPS for sourceforge.net projects
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2023-11-06 11:03:47 +01:00 |
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muscle
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ncbi-blast+
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devel/grpc: Update to 1.65.4
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2024-08-15 18:55:25 +08:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: update 28.0.7 → 28.0.8
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2024-09-07 21:10:05 -07:00 |
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ncbi-entrez-direct
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all: Bump after lang/go121 update
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2024-08-09 06:24:08 +00:00 |
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ncbi-toolkit
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MANPREFIX: eliminate its usage
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2024-01-12 16:11:29 +01:00 |
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ncbi-vdb
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*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Attempt to fix build on i386
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2024-04-28 00:10:02 -07:00 |
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8
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2023-12-25 16:59:52 +08:00 |
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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biology/p5-BioPerl: Update to 1.007008
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2023-10-11 20:57:41 +08:00 |
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p5-BioPerl-Run
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p5-transdecoder
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p5-transdecoder: Update to 5.7.1
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2023-08-05 15:58:40 -05:00 |
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p5-TrimGalore
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biology/p5-TrimGalore: Update to 0.6.10
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2024-07-23 11:01:28 -04:00 |
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paml
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biology/paml: Update to 4.10.7
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2023-07-08 00:46:53 -03:00 |
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pbbam
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biology/pbbam: Bump PORTREVISION for biology/htslib update
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2023-01-05 19:25:09 -06:00 |
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peak-classifier
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biology/peak-classifier: Clean up USES=python
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2024-04-05 08:43:40 +08:00 |
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pear-merger
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MANPREFIX: eliminate its usage
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2024-01-12 16:11:29 +01:00 |
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phrap
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phred
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phyml
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biology/phyml: fix build on non-amd64
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2024-06-16 17:25:18 +02:00 |
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picard-tools
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*/*: Refactor java/openjdk7 removal
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2023-04-04 13:10:53 -05:00 |
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plink
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*/*: bump PORTREVISION after the upgrade to OpenBLAS
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2024-06-21 19:49:24 +02:00 |
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pooler
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biology/pooler: Moved man to share/man
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2024-02-22 14:23:50 +01:00 |
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primer3
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biology/primer3: Fix build with llvm16
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2023-08-05 20:55:50 +02:00 |
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prodigal
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biology/prodigal: Update 2.6.3-7 → 2.6.3-16
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2023-07-22 00:37:33 -07:00 |
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prodigy-lig
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biology/prodigy-lig: update 1.1.0 → 1.1.1
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2024-04-26 22:55:21 -07:00 |
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protomol
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graphics/tiff: Update to 4.6.0
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2024-04-27 14:44:59 +02:00 |
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psi88
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*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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py-bcbio-gff
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biology/py-bcbio-gff: Update to 0.7.0
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2023-03-16 17:32:06 -05:00 |
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py-biom-format
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biology/py-biom-format: update 2.1.10 → 2.1.16
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2024-07-13 11:06:57 -07:00 |
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py-biopython
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biology/py-biopython: Update to 1.83
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2024-04-08 02:29:37 +00:00 |
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py-biosig
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biology/{.py-}biosig: update 2.6.0 → 2.6.1
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2024-08-05 07:37:01 -07:00 |
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py-bx-python
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biology/py-bx-python: update 0.10.0 → 0.11.0
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2024-02-12 15:07:35 -08:00 |
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py-crossmap
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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py-cutadapt
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biology/py-cutadapt: update to 4.9
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2024-06-20 10:38:00 +02:00 |
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py-deeptools
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biology/py-deeptools: Update to 3.5.2
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2023-06-19 07:09:17 -05:00 |
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py-deeptoolsintervals
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*/*: rename CHEESESHOP to PYPI in MASTER_SITES
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2023-01-11 18:58:34 +03:00 |
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py-dna-features-viewer
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biology/py-dna-features-viewer: Update to 3.1.3
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2023-11-04 17:11:34 -05:00 |
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py-dnaio
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biology/py-dnaio: Update to 1.2.1
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2024-07-04 09:15:39 +00:00 |
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py-ete3
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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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py-Genesis-PyAPI
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biology/py-Genesis-PyAPI: Add NO_ARCH
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2023-08-01 00:42:07 +08:00 |
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py-gffutils
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biology/py-gffutils: update 0.11.1 → 0.13
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2024-06-16 18:20:35 -07:00 |
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py-goatools
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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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py-gtfparse
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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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py-hits
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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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py-htseq
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biology/py-htseq: Fix build with python-3.11
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2024-01-21 07:13:35 +00:00 |
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py-libnuml
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biology/py-libnuml: Allow build with swig 4.1.0+
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2023-04-19 02:05:12 +08:00 |
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py-libsedml
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biology/py-libsedml: Allow build with swig 4.1.0+
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2023-04-19 02:05:12 +08:00 |
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py-loompy
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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py-macs2
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biology/py-macs2: Update to 2.2.9.1
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2023-08-06 13:17:52 -05:00 |
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py-macs3
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all: drop support for FreeBSD 13.2 which reached EOL today
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2024-07-01 22:27:23 +02:00 |
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py-mrcfile
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biology/py-mrcfile: update 1.5.2 → 1.5.3
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2024-07-26 01:57:55 -07:00 |
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py-multiqc
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devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml
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2024-07-07 16:05:33 +08:00 |
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py-newick
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biology/py-newick: Add new port
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2024-02-03 00:58:29 +00:00 |
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py-ont-fast5-api
|
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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py-orange3-bioinformatics
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devel/py-setuptools-scm: update to 8.0.4
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2024-02-29 02:18:32 -05:00 |
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py-orange3-single-cell
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biology/py-orange3-single-cell: Add NO_ARCH
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2023-08-01 00:42:07 +08:00 |
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py-pandas-charm
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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py-py2bit
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*/*: rename CHEESESHOP to PYPI in MASTER_SITES
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2023-01-11 18:58:34 +03:00 |
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py-pybigwig
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biology/py-pybigwig: Update to 0.3.22
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2023-12-16 07:59:37 -06:00 |
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py-pyfaidx
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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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py-pyrodigal
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biology/py-pyrodigal: update 3.5.1 → 3.5.2
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2024-09-05 01:48:51 -07:00 |
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py-pysam
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biology/py-pysam: update 0.22.0 → 0.22.1
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2024-04-25 07:52:08 -07:00 |
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py-PySCeS
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biology/py-PySCeS: update 1.2.1 → 1.2.2
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2024-08-03 01:27:31 -07:00 |
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py-python-libsbml
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biology/py-python-libsbml: relax python version requirement
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2023-12-03 15:02:23 +03:00 |
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py-pywgsim
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biology/py-pywgsim: fix build
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2024-06-07 11:11:35 +03:00 |
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py-resdk
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biology/py-resdk: update 21.1.0 → 21.2.0
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2024-07-12 01:58:00 -07:00 |
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py-scikit-bio
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biology/py-scikit-bio: update 0.6.1 → 0.6.2
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2024-07-12 22:17:53 -07:00 |
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py-valerius
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biology/py-valerius: New port: Python bioinformatics tools
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2022-10-03 21:06:22 -07:00 |
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py-xenaPython
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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pyfasta
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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python-nexus
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biology/python-nexus: Update to 2.9.0 and fix build with python-3.11
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2024-02-03 00:58:29 +00:00 |
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R-cran-Biobase
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biology/R-cran-Biobase: New port
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2023-12-15 13:55:44 +01:00 |
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R-cran-BiocGenerics
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biology/R-cran-BiocGenerics: New port
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2023-12-15 13:55:44 +01:00 |
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R-cran-BiocManager
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biology/R-cran-BiocManager: Update version 1.30.24=>1.30.25
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2024-09-08 19:28:55 +02:00 |
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rainbow
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rampler
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*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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readseq
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rna-seq
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biology/rna-seq: Add biology/star dep to metaport
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2023-07-31 09:36:06 -05:00 |
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ruby-bio
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Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby
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2023-01-14 17:08:33 -06:00 |
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rubygem-bio
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biology/rubygem-bio: Update to 2.0.5
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2023-09-30 08:46:30 +08:00 |
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rubygem-bio-executables
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Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby
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2023-01-14 17:08:33 -06:00 |
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rubygem-bio-old-biofetch-emulator
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Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby
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2023-01-14 17:08:33 -06:00 |
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rubygem-bio-shell
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Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby
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2023-01-14 17:08:33 -06:00 |
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salmon
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devel/onetbb: Update to 2021.13.0
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2024-07-04 13:39:44 +02:00 |
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sam2pairwise
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samtools
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biology/samtools: Move man pages to share/man
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2024-03-02 19:40:58 +00:00 |
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scrm
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biology/scrm: Move man pages to share/man
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2024-03-02 19:59:23 +00:00 |
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seaview
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MANPREFIX: eliminate its usage
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2024-01-12 16:11:29 +01:00 |
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seqan
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seqan1
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seqan3
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biology/seqan3: update 3.2.0 → 3.3.0
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2023-09-10 11:10:47 -07:00 |
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seqan-apps
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biology/seqan-apps: Fix build with llvm16
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2023-08-06 23:53:04 +02:00 |
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seqkit
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all: Bump after lang/go121 update
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2024-08-09 06:24:08 +00:00 |
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seqtk
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biology/seqtk: Update to 1.4
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2023-05-23 17:42:13 -05:00 |
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seqwish
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biology/seqwish: update 0.7.9 → 0.7.10
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2024-05-18 10:29:58 -07:00 |
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sigviewer
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*: Bump PORTREVISIONs for math/mpc update to 1.3.1
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2023-04-23 09:09:58 +00:00 |
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slclust
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smithwaterman
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snpeff
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*/*: Update WWW to use HTTPS for sourceforge.net projects
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2023-11-06 11:03:47 +01:00 |
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spoa
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biology/spoa: Broken on i386
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2024-04-11 21:05:12 -07:00 |
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sra-tools
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cleanup: remove occurrences of WITH_DEBUG
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2024-04-12 08:04:05 +02:00 |
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stacks
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biology/stacks: Unbreak build on aarch64
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2024-05-28 16:17:25 -05:00 |
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star
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biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
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2024-05-05 09:58:47 -05:00 |
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stringtie
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subread
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tabixpp
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biology/tabixpp: Deprecate
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2023-01-22 11:01:57 -06:00 |
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taxonkit
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all: Bump after lang/go121 update
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2024-08-09 06:24:08 +00:00 |
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treekin
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biology/treekin: Move man pages to share/man
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2024-03-02 20:02:27 +00:00 |
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treepuzzle
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trimadap
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biology/trimadap: drop GCC requirement on powerpc64le
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2023-08-03 10:40:03 +00:00 |
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trimmomatic
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biology/trimmomatic: Release to ports@
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2024-04-05 19:12:17 -05:00 |
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tRNAscan-SE
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biology/tRNAscan-SE: Update to 2.0.11
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2022-10-12 12:45:24 +01:00 |
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ucsc-userapps
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biology/ucsc-userapps: Replace dependencies
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2023-12-30 08:16:41 +01:00 |
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ugene
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MAN?PREFIX: eleminate its usage and move man to share/man
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2024-01-10 09:16:01 +01:00 |
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unikmer
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all: Bump after lang/go121 update
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2024-08-09 06:24:08 +00:00 |
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vcf2hap
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biology/vcf2hap: Move man pages to share/man
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2024-03-02 20:07:47 +00:00 |
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vcf-split
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biology/vcf-split: Move man pages to share/man
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2024-03-02 20:04:57 +00:00 |
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vcflib
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biology/vcflib: add upstream reference for zig >= 0.11
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2024-05-20 16:42:43 +02:00 |
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vcftools
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biology/vcftools: Move man pages to share/man
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2024-03-02 20:35:56 +00:00 |
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velvet
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viennarna
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biology/viennarna: Move man pages to share/man
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2024-03-02 20:35:56 +00:00 |
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vsearch
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biology/vsearch: Update to 2.28.1
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2024-05-01 08:41:05 -05:00 |
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vt
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biology/vt: Bump PORTREVISION for biology/htslib update
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2023-01-05 19:19:19 -06:00 |
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wfa2-lib
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biology/wfa2-lib: fix build without libomp
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2024-08-04 14:00:47 +02:00 |
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wise
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*/*: Fix build with llvm16 on 13.2-STABLE
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2023-07-26 02:48:20 +02:00 |
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Makefile
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biology/andi: New ports: Efficient estimation of evolutionary distances
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2024-09-07 14:31:10 -07:00 |
