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abyss
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biology/abyss: Move man pages to share/man
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2024-03-03 10:04:08 +00:00 |
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ad2vcf
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biology/ad2vcf: Move man pages to share/man
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2024-03-02 18:32:34 +00:00 |
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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 PORTREVISION after the upgrade to SuiteSparse
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2024-01-28 13:02:23 +01:00 |
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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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bamutil
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barrnap
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bbmap
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bcf-score
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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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bioawk
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biococoa
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biolibc
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biology/biolibc: Impelled to share/man
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2024-01-23 15:51:25 +01:00 |
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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 2.5.2 → 2.6.0
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2024-04-05 18:04:45 -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 1.10.1_3
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2024-02-16 07:42:11 -06:00 |
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bolt-lmm
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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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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 2.5.3
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2024-01-18 17:20:08 -06:00 |
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btllib
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biology/btllib: update 1.7.1 → 1.7.2
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2024-04-09 00:40:58 -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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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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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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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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ddocent
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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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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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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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*/*: Replace format=bsdtar with format=ustar in tar archive operations
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2024-02-18 17:48:08 -08:00 |
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gcta
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biology/gcta: chase the upgrade of OpenBLAS
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2023-12-12 20:03:50 +01:00 |
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gemma
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*/*: bump PORTREVISION after the upgrade of OpenBLAS
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2023-12-12 20:03:50 +01:00 |
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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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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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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 2.5.60
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2024-04-14 18:14:19 -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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biology/iqtree: Update to 2.3.2
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2024-04-14 16:38:43 -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 0.50.1,1
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2023-11-04 08:15:25 -05:00 |
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kmcp
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all: Bump after lang/go121 update
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2024-04-15 08:20:04 +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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libgff
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libgtextutils
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libneurosim
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libnuml
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libsbml
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biology/libsbml: Update to 5.20.2
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2023-09-30 08:44:19 +08:00 |
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libsedml
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linux-foldingathome
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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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metaeuk
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biology/metaeuk: Broken on powerpc64le
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2024-02-04 10:27:53 -08:00 |
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migrate
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biology/migrate: Use system zlib instead of excluding it from extract
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2024-04-12 21:07:33 +01:00 |
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minimap2
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biology/minimap2: Fix man prefix
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2024-04-17 17:52:15 -05:00 |
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mmseqs2
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molden
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mothur
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biology/mothur: Remove CC/CPP/CXX exports
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2023-09-28 20:56:25 +02:00 |
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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 1.62.0
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2024-03-09 22:05:20 +08:00 |
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ncbi-cxx-toolkit
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graphics/proj: Update to 9.4.0
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2024-04-15 06:44:23 +02:00 |
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ncbi-entrez-direct
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all: Bump after lang/go121 update
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2024-04-15 08:20:04 +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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ngs-sdk
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biology/ngs-sdk: Not for powerpc, powerpc64le
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2024-02-02 13:33:37 -08:00 |
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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: Release to ports@
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2024-04-05 19:12:17 -05:00 |
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paml
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pbbam
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pbseqan
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biology/pbseqan: Set EXPIRATION_DATE
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2024-04-04 18:35:51 +02:00 |
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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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picard-tools
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plink
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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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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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prodigy-lig
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biology/prodigy-lig: update 1.0.1 → 1.1.0
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2024-03-21 03:08:33 -07:00 |
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protomol
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*/*: Update WWW to use HTTPS for sourceforge.net projects
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2023-11-01 23:11:47 +01:00 |
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psi88
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py-bcbio-gff
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py-biom-format
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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 2.5.2 → 2.6.0
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2024-04-05 18:04:45 -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: Release to ports@
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2024-04-05 19:12:16 -05:00 |
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py-deeptools
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py-deeptoolsintervals
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py-dna-features-viewer
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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: Release to ports@
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2024-04-10 18:41:31 -05:00 |
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py-ete3
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py-Genesis-PyAPI
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py-gffutils
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py-goatools
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py-gtfparse
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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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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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biology/py-macs3: Mark not for i386
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2024-04-18 18:02:57 -05:00 |
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py-mrcfile
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biology/py-mrcfile: update 1.4.3 → 1.5.0
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2024-01-19 23:47:54 -08:00 |
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py-multiqc
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biology/py-multiqc: Update to 1.15
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2023-08-05 11:18:37 -05:00 |
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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 3.2.2 → 3.3.0
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2024-03-08 14:34:40 -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: Fix build by adding USES=localbase:ldflags
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2023-12-14 00:43:06 -08:00 |
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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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py-resdk
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biology/py-resdk: update 20.0.0 → 21.1.0
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2024-04-05 18:04:45 -07:00 |
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py-scikit-bio
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biology/py-scikit-bio: update 0.5.9 → 0.6.0
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2024-04-05 18:04:46 -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: New port
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2023-12-15 13:55:43 +01:00 |
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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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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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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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salmon
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devel/onetbb: Update to 2021.12.0
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2024-04-17 13:28:34 +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
|
all: Bump after lang/go121 update
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2024-04-15 08:20:04 +00:00 |
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seqtk
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seqwish
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biology/seqwish: Add comment
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2023-11-05 15:07:52 -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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*/*: 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
|
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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star
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biology/star: Fix SIMD issue on non-amd64
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2023-08-21 09:33:20 -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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all: Bump after lang/go121 update
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2024-04-15 08:20:04 +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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ucsc-userapps
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biology/ucsc-userapps: Replace dependencies
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2023-12-30 08:16:41 +01:00 |
|
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
|
all: Bump after lang/go121 update
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2024-04-15 08:20:04 +00:00 |
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vcf2hap
|
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
|
biology/vcf-split: Move man pages to share/man
|
2024-03-02 20:04:57 +00:00 |
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vcflib
|
biology/vcflib: Update to 1.0.10
|
2024-04-22 07:42:04 -05:00 |
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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 2.27.1
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2024-04-08 16:43:20 -05:00 |
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vt
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wfa2-lib
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biology/wfa2-lib: Update to 2.3.5
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2024-04-22 07:42:04 -05:00 |
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wise
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Makefile
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biology/py-newick: Add new port
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2024-02-03 00:58:29 +00:00 |
