| .. |
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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 to SuiteSparse
|
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
|
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: 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: 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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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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*/*: bump PORTREVISION after the upgrade to SuiteSparse
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2024-01-28 13:02:23 +01:00 |
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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
|
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 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: 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
|
2024-01-09 16:41:04 +01:00 |
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fasta3
|
MAN?PREFIX: eleminate its usage and move man to share/man
|
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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*/*: Replace format=bsdtar with format=ustar in tar archive operations
|
2024-02-18 17:48:08 -08:00 |
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gcta
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biology/gcta: chase the upgrade of OpenBLAS
|
2023-12-12 20:03:50 +01:00 |
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gemma
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*/*: bump PORTREVISION after the upgrade of OpenBLAS
|
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 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
|
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
|
2024-01-27 13:37:30 +01:00 |
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hyphy
|
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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biology/infernal: Moved man to share/man
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2024-02-22 14:23:47 +01:00 |
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iolib
|
biology/iolib: Moved man to share/man
|
2024-02-22 14:23:48 +01:00 |
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iqtree
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biology/iqtree: Update to 2.2.2.7
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2023-09-04 23:45:37 -03:00 |
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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
|
2024-02-11 10:39:17 +00:00 |
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lamarc
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libbigwig
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biology/libbigwig: Fix name-clashing in roundup
|
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
|
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
|
2023-12-13 23:11:55 -08:00 |
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mafft
|
biology/mafft: Moved man to share/man
|
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
|
2024-01-12 17:57:41 -08:00 |
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megahit
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metaeuk
|
biology/metaeuk: Broken on powerpc64le
|
2024-02-04 10:27:53 -08:00 |
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migrate
|
MAN[1-5]PREFIX: eleminate its usage and move man to share/man
|
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
|
2023-09-28 20:56:25 +02:00 |
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mrbayes
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mummer
|
*/*: Update WWW to use HTTPS for sourceforge.net projects
|
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 1.61.1
|
2024-02-21 23:06:22 +08:00 |
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ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Broken on armv7
|
2024-01-20 20:09:20 -08:00 |
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ncbi-entrez-direct
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
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ncbi-toolkit
|
MANPREFIX: eliminate its usage
|
2024-01-12 16:11:29 +01:00 |
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ncbi-vdb
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ngs-sdk
|
biology/ngs-sdk: Not for powerpc, powerpc64le
|
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
|
biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8
|
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
|
biology/p5-BioPerl: Update to 1.007008
|
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
|
biology/peak-classifier: Update to 0.1.4.13
|
2023-10-28 06:38:43 -05:00 |
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pear-merger
|
MANPREFIX: eliminate its usage
|
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
|
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
|
2023-12-31 01:37:05 +01:00 |
|
pooler
|
biology/pooler: Moved man to share/man
|
2024-02-22 14:23:50 +01:00 |
|
primer3
|
|
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prodigal
|
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prodigy-lig
|
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protomol
|
*/*: Update WWW to use HTTPS for sourceforge.net projects
|
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
|
*/*: Update WWW to use HTTPS for sourceforge.net projects
|
2023-11-06 11:03:47 +01:00 |
|
py-bx-python
|
biology/py-bx-python: update 0.10.0 → 0.11.0
|
2024-02-12 15:07:35 -08:00 |
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py-crossmap
|
|
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py-cutadapt
|
biology/py-cutadapt: Update to 4.6
|
2024-02-06 06:55:32 -06:00 |
|
py-deeptools
|
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py-deeptoolsintervals
|
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py-dna-features-viewer
|
biology/py-dna-features-viewer: Update to 3.1.3
|
2023-11-04 17:11:34 -05:00 |
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py-dnaio
|
biology/py-dnaio: Update to 1.2.0
|
2024-02-06 06:51:39 -06:00 |
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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
|
biology/py-htseq: Fix build with python-3.11
|
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
|
biology/py-macs3: Peak caller for TF binding sites
|
2024-01-10 09:19:56 -06:00 |
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py-mrcfile
|
biology/py-mrcfile: update 1.4.3 → 1.5.0
|
2024-01-19 23:47:54 -08:00 |
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py-multiqc
|
|
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|
py-newick
|
biology/py-newick: Add new port
|
2024-02-03 00:58:29 +00:00 |
|
py-ont-fast5-api
|
|
|
|
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
|
biology/py-pybigwig: Update to 0.3.22
|
2023-12-16 07:59:37 -06:00 |
|
py-pyfaidx
|
|
|
|
py-pyrodigal
|
biology/py-pyrodigal: update 3.2.1 → 3.2.2
|
2024-01-21 01:44:54 -08:00 |
|
py-pysam
|
biology/py-pysam: relax python version requirement
|
2023-12-03 14:51:05 +03:00 |
|
py-PySCeS
|
biology/py-PySCeS: Fix build by adding USES=localbase:ldflags
|
2023-12-14 00:43:06 -08:00 |
|
py-python-libsbml
|
biology/py-python-libsbml: relax python version requirement
|
2023-12-03 15:02:23 +03:00 |
|
py-pywgsim
|
|
|
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py-resdk
|
biology/py-resdk: relax chardet limitation
|
2023-12-08 21:55:13 +01:00 |
|
py-scikit-bio
|
|
|
|
py-valerius
|
|
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|
py-xenaPython
|
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pyfasta
|
|
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python-nexus
|
biology/python-nexus: Update to 2.9.0 and fix build with python-3.11
|
2024-02-03 00:58:29 +00:00 |
|
R-cran-Biobase
|
biology/R-cran-Biobase: New port
|
2023-12-15 13:55:44 +01:00 |
|
R-cran-BiocGenerics
|
biology/R-cran-BiocGenerics: New port
|
2023-12-15 13:55:44 +01:00 |
|
R-cran-BiocManager
|
biology/R-cran-BiocManager: New port
|
2023-12-15 13:55:43 +01:00 |
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rainbow
|
|
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|
rampler
|
|
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|
readseq
|
|
|
|
rna-seq
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
biology/rubygem-bio: Update to 2.0.5
|
2023-09-30 08:46:30 +08:00 |
|
rubygem-bio-executables
|
|
|
|
rubygem-bio-old-biofetch-emulator
|
|
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|
rubygem-bio-shell
|
|
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|
salmon
|
devel/onetbb: Update to 2021.11.0
|
2023-11-28 12:35:02 +01:00 |
|
sam2pairwise
|
|
|
|
samtools
|
|
|
|
scrm
|
|
|
|
seaview
|
MANPREFIX: eliminate its usage
|
2024-01-12 16:11:29 +01:00 |
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan3
|
biology/seqan3: update 3.2.0 → 3.3.0
|
2023-09-10 11:10:47 -07:00 |
|
seqan-apps
|
|
|
|
seqkit
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
seqtk
|
|
|
|
seqwish
|
biology/seqwish: Add comment
|
2023-11-05 15:07:52 -08:00 |
|
sigviewer
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
snpeff
|
*/*: Update WWW to use HTTPS for sourceforge.net projects
|
2023-11-06 11:03:47 +01:00 |
|
spoa
|
biology/spoa: update 4.0.7 → 4.1.0
|
2023-08-29 09:59:01 -07:00 |
|
sra-tools
|
|
|
|
stacks
|
|
|
|
star
|
|
|
|
stringtie
|
|
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subread
|
|
|
|
tabixpp
|
|
|
|
taxonkit
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
treekin
|
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
|
2024-01-01 12:49:51 +01:00 |
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ucsc-userapps
|
biology/ucsc-userapps: Replace dependencies
|
2023-12-30 08:16:41 +01:00 |
|
ugene
|
MAN?PREFIX: eleminate its usage and move man to share/man
|
2024-01-10 09:16:01 +01:00 |
|
unikmer
|
all: Bump PORTREVISION after lang/go* update
|
2024-02-11 10:39:17 +00:00 |
|
vcf2hap
|
biology/vcf2hap: Update to 0.1.6.7
|
2023-10-28 06:44:44 -05:00 |
|
vcf-split
|
biology/vcf-split: Update to 0.1.5.10
|
2023-10-28 06:41:39 -05:00 |
|
vcflib
|
lang/zig: update to 0.11.0
|
2024-01-01 06:37:19 +01:00 |
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
|
2024-01-01 12:49:51 +01:00 |
|
vsearch
|
biology/vsearch: Update to 2.27.0
|
2024-01-23 07:16:13 -06:00 |
|
vt
|
|
|
|
wfa2-lib
|
biology/wfa2-lib: Update to 2.3.4
|
2023-09-29 13:24:07 -05:00 |
|
wise
|
|
|
|
Makefile
|
biology/py-newick: Add new port
|
2024-02-03 00:58:29 +00:00 |
