| .. |
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abyss
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biology/abyss: update 2.3.9 → 2.3.10
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2024-11-04 12:36:54 -08:00 |
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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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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +03:00 |
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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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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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bbmap
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bcf-score
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biology/bcf-score: Update to 1.20
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2024-10-09 17:23:09 -05:00 |
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bcftools
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biology/bcftools: Update to 1.21
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2024-10-09 17:23:09 -05:00 |
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bedtools
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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 1.20
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2024-10-09 17:23:10 -05:00 |
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bioawk
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biococoa
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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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biosig
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biology/biosig: fix build with libc++ 19
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2024-10-11 19:30:49 +02:00 |
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biosoup
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biostar-tools
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biology/biostar-tools: Update to 2.0
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2024-11-07 18:44:28 -06:00 |
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bolt-lmm
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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +03:00 |
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bowtie
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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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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +03:00 |
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cd-hit
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cdbfasta
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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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clustal-omega
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clustalw
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coverm
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lang/rust: Bump revisions after 1.82.0
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2024-11-08 09:24:20 +01:00 |
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cufflinks
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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +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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diamond
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biology/diamond: Update to v2.1.10
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2024-10-25 13:20:52 -03:00 |
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dsr-pdb
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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +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: remove maintainer (email address gone)
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2024-10-28 13:41:54 +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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fastani
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biology/fastani: Broken where OpenMP isn't available; Update WWW
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2024-11-02 23:47:52 -07:00 |
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fastdnaml
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fastool
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fastp
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biology/fastp: Update to 0.24.0
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2024-11-16 07:10:58 -06:00 |
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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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fasttree
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fastx-toolkit
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fermi-lite
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biology/fermi-lite: port to armv7/aarch64
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2024-10-28 13:41:48 +01:00 |
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figtree
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flash
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fluctuate
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freebayes
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garlic
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gatk
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biology/gatk: Update TEST_ENV
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2024-11-01 12:29:28 -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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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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graphlan
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groopm
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haplohseq
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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +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: update to 3.4
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2024-10-28 13:41:48 +01:00 |
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htslib
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biology/htslib: Update to 1.21
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2024-10-09 17:23:08 -05:00 |
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hyphy
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biology/hyphy: Update to 2.5.62
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2024-10-25 13:20:53 -03:00 |
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igv
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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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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +03:00 |
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jalview
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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 0.51.1,1
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2024-09-19 17:46:47 -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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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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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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textproc/xerces-c3: Update to 3.3.0
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2024-10-25 23:56:41 +08:00 |
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libsedml
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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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mca-calling
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biology/mca-calling: Core tools for mCA event calling
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2024-10-24 08:32:05 -05:00 |
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megahit
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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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mothur
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biology/mothur: update 1.48.1 → 1.48.2
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2024-11-04 23:25:49 -08:00 |
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mrbayes
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mummer
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biology/mummer: update 4.0.0beta2-2 → 4.0.0rc1.20240427
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2024-10-31 12:28:12 -07:00 |
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muscle
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ncbi-blast+
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Bump PORTREVISIONs after grpc shlib change in 2715f16944
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2024-11-11 23:13:54 -04:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: update 28.0.9 → 28.0.10
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2024-11-13 08:42:21 -08:00 |
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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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all: drop support for expired FreeBSD 14.0
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2024-10-01 20:56:20 +02:00 |
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ncbi-vdb
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biology/ncbi-vdb: Deprecate and set expiration date to 2024-12-31
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2024-11-06 20:39:54 +01:00 |
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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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p5-BioPerl-Run
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p5-transdecoder
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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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pbbam
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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +03:00 |
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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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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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prodigal
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prodigy-lig
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biology/prodigy-lig: update 1.1.2 → 1.1.3
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2024-10-15 08:33:52 -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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py-bcbio-gff
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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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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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py-deeptoolsintervals
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py-dna-features-viewer
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py-dnaio
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biology/py-dnaio: Update to 1.2.2
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2024-10-24 08:09:54 +00:00 |
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py-ete3
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py-Genesis-PyAPI
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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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py-gtfparse
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biology/py-gtfparse: update 1.3.0 → 2.5.0
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2024-11-16 02:27:19 -08:00 |
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py-hits
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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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py-libsedml
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py-loompy
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py-macs2
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py-macs3
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biology/py-macs3: Update to 3.0.2
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2024-09-14 08:23:32 -05:00 |
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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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biology/py-multiqc: Update to 1.25.1
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2024-11-15 19:28:59 -06:00 |
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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
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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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py-pandas-charm
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py-py2bit
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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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py-pyrodigal
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biology/py-pyrodigal: update 3.5.2 → 3.6.3
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2024-11-12 00:32:35 -08:00 |
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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: update 5.20.1 → 5.20.4
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2024-11-12 02:18:13 -08:00 |
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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 21.2.0 → 21.2.1
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2024-11-10 19:54:22 -08:00 |
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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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py-xenaPython
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pyfasta
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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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readseq
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rna-seq
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ruby-bio
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rubygem-bio
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rubygem-bio-executables
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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salmon
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*/*: bump consumers after devel/boost* update
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2024-10-03 13:25:14 +03:00 |
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sam2pairwise
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samtools
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biology/samtools: Update to 1.21
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2024-10-09 17:23:09 -05:00 |
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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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seqan-apps
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seqkit
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biology/seqkit: update 2.8.2 → 2.9.0
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2024-11-04 17:26:42 -08:00 |
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seqtk
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seqwish
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biology/seqwish: Broken on 15 with clng-19
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2024-11-16 02:27:18 -08:00 |
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sigviewer
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slclust
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smithwaterman
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snpeff
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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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biology/sra-tools: Quick fix to unbreak build
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2024-11-16 08:56:44 -06:00 |
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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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taxonkit
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biology/taxonkit: update 0.17.0 → 0.18.0
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2024-11-04 17:26:41 -08:00 |
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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: Update to 0.1.4
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2024-10-18 06:37:12 -05:00 |
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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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ucsc-userapps
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biology/ucsc-userapps: remove ONLY_FOR_ARCHS
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2024-11-14 09:41:02 +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: Broken on 15
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2024-11-02 01:51:51 -07:00 |
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vsearch
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biology/vsearch: Update to 2.29.1
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2024-10-27 17:51:28 -05:00 |
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vt
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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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all: drop support for expired FreeBSD 14.0
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2024-10-01 20:56:20 +02:00 |
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Makefile
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biology/mca-calling: Core tools for mCA event calling
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2024-10-24 08:32:05 -05:00 |
