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abyss
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*/*: bump PORTREVISION after the upgrade of MPICH to 4.1.2
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2023-12-10 11:23:11 +01:00 |
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ad2vcf
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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 of SuiteSparse to v7.5.0
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2024-01-13 11:19:22 +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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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 1.3.1
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2023-11-21 06:58:39 -06:00 |
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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: Update to 0.2.6
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2023-10-28 06:21:35 -05:00 |
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biolibc-tools
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biology/biolibc-tools: Update to 0.1.4.13
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2023-10-29 17:41:02 -05:00 |
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bioparser
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biosig
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*/*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0
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2024-01-13 11:19:22 +01:00 |
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biosoup
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biostar-tools
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bolt-lmm
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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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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: Temporarily not for non-64-bit architectures
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2024-01-11 19:01:51 -08:00 |
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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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cdbfasta
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checkm
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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 all consumers after 1.83.0
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2023-09-27 17:36:30 +03:00 |
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cytoscape
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ddocent
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diamond
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biology/diamond: Fix build on main after import of clang 17
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2023-12-29 14:57:14 -04:00 |
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dsr-pdb
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devel/boost*: bump all consumers after 1.83.0
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2023-09-27 17:36:30 +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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fasda
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biology/fasda: Update to 0.1.5
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2023-10-28 06:32:20 -05:00 |
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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: Update to 0.1.3
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2023-10-28 06:34:21 -05:00 |
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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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*/*: 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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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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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 all consumers after 1.83.0
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2023-09-27 17:36:30 +03:00 |
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hhsuite
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hisat2
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hmmer
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htslib
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hyphy
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biology/hyphy: Update to 2.5.58
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2023-12-23 13:28:25 -04:00 |
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igv
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infernal
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iolib
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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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iqtree
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jalview
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jellyfish
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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 PORTREVISION after lang/go* update
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2023-12-07 02:22:10 +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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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: Fix build on 14.x and main
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2023-12-13 23:11:55 -08:00 |
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mafft
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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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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: fix build on powerpc64le by disabling openmp until libomp is fixed
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2024-01-16 15:35:21 +01:00 |
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migrate
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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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minimap2
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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 1.60.0
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2023-12-15 01:03:10 +08:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: Broken on armv7
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2024-01-20 20:09:20 -08:00 |
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ncbi-entrez-direct
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all: Bump PORTREVISION after lang/go* update
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2023-12-07 02:22:10 +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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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-TrimGalore
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paml
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pbbam
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pbseqan
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peak-classifier
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biology/peak-classifier: Update to 0.1.4.13
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2023-10-28 06:38:43 -05:00 |
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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: Update to 1.88
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2023-09-10 08:06:18 -05:00 |
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primer3
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prodigal
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prodigy-lig
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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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py-biosig
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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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py-bx-python
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py-crossmap
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py-cutadapt
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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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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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py-macs3
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biology/py-macs3: Peak caller for TF binding sites
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2024-01-10 09:19:56 -06:00 |
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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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py-ont-fast5-api
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py-orange3-bioinformatics
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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 3.2.1 → 3.2.2
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2024-01-21 01:44:54 -08:00 |
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py-pysam
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biology/py-pysam: relax python version requirement
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2023-12-03 14:51:05 +03:00 |
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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: relax chardet limitation
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2023-12-08 21:55:13 +01:00 |
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py-scikit-bio
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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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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 2021.11.0
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2023-11-28 12:35:02 +01:00 |
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sam2pairwise
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samtools
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scrm
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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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seqkit
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all: Bump PORTREVISION after lang/go* update
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2023-12-07 02:22:10 +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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sra-tools
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stacks
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star
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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 0.15.0 → 0.15.1
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2023-12-19 23:02:18 -08:00 |
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treekin
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*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
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2024-01-01 12:49:51 +01:00 |
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treepuzzle
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trimadap
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trimmomatic
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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 |
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ugene
|
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 PORTREVISION after lang/go* update
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2023-12-07 02:22:10 +00:00 |
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vcf2hap
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biology/vcf2hap: Update to 0.1.6.7
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2023-10-28 06:44:44 -05:00 |
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vcf-split
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biology/vcf-split: Update to 0.1.5.10
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2023-10-28 06:41:39 -05:00 |
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vcflib
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lang/zig: update to 0.11.0
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2024-01-01 06:37:19 +01:00 |
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vcftools
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velvet
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viennarna
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*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
|
2024-01-01 12:49:51 +01:00 |
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vsearch
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biology/vsearch: Update to 2.26.1
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2023-11-26 06:32:55 -06:00 |
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vt
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wfa2-lib
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biology/wfa2-lib: Update to 2.3.4
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2023-09-29 13:24:07 -05:00 |
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wise
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Makefile
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biology/recombine: Remove expired port
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2024-01-18 22:23:16 +01:00 |
