| .. |
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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
|
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
|
2024-01-13 11:19:22 +01:00 |
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avida
|
*/*: 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
|
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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biology/bcf-score: Unbreak build with clang 16
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2023-07-16 08:19:06 -05:00 |
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bcftools
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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
|
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
|
2023-10-29 17:41:02 -05:00 |
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bioparser
|
biology/bioparser: update 3.0.15 → 3.1.0
|
2023-08-29 00:32:45 -07:00 |
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biosig
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*/*: bump PORTREVISION after the upgrade of SuiteSparse to v7.5.0
|
2024-01-13 11:19:22 +01:00 |
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biosoup
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biology/biosoup: Install cmake files
|
2023-08-29 00:32:45 -07:00 |
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biostar-tools
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bolt-lmm
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*/*: bump PORTREVISION after the upgrade of OpenBLAS
|
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
|
2023-11-06 11:03:47 +01:00 |
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bowtie2
|
biology/bowtie2: Update to 2.5.3
|
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
|
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
|
2024-01-10 09:16:01 +01:00 |
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canu
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biology/canu: Fix build with llvm16
|
2023-07-20 19:42:34 +02:00 |
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cd-hit
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biology/cd-hit: allow to build without GCC on libomp-less systems
|
2023-08-12 03:37:47 +02:00 |
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cdbfasta
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biology/cdbfasta: Update to 2023.07.10
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2023-07-11 10:40:27 -05:00 |
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checkm
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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chip-seq
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clustal-omega
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clustalw
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biology/clustalw: Unbreak build for clang 16
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2023-07-15 18:18:42 -05:00 |
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cufflinks
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devel/boost*: bump 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
|
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
|
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
|
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
|
2023-12-31 01:37:05 +01:00 |
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gcta
|
biology/gcta: chase the upgrade of OpenBLAS
|
2023-12-12 20:03:50 +01:00 |
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gemma
|
*/*: 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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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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haplohseq
|
devel/boost*: bump all consumers after 1.83.0
|
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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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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htslib
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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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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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iolib
|
*/*: Update WWW to use HTTPS for sourceforge.net projects
|
2023-11-01 23:11:47 +01:00 |
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iqtree
|
biology/iqtree: Update to 2.2.2.7
|
2023-09-04 23:45:37 -03:00 |
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jalview
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jellyfish
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kallisto
|
biology/kallisto: Update to 0.50.1,1
|
2023-11-04 08:15:25 -05:00 |
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kmcp
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all: Bump PORTREVISION after lang/go* update
|
2023-12-07 02:22:10 +00:00 |
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lamarc
|
biology/lamarc: Mark BROKEN on 14
|
2023-08-18 08:57:13 +02:00 |
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libbigwig
|
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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all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
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libnuml
|
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libsbml
|
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
|
biology/locarna: Fix build on 14.x and main
|
2023-12-13 23:11:55 -08:00 |
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mafft
|
*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree
|
2023-12-31 01:37:05 +01:00 |
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mapm3
|
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mashmap
|
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: fix build on powerpc64le by disabling openmp until libomp is fixed
|
2024-01-16 15:35:21 +01:00 |
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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
|
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+
|
devel/grpc: Update to 1.60.0
|
2023-12-15 01:03:10 +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
|
2023-12-07 02:22:10 +00:00 |
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ncbi-toolkit
|
MANPREFIX: eliminate its usage
|
2024-01-12 16:11:29 +01:00 |
|
ncbi-vdb
|
|
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ngs-sdk
|
biology/ngs-sdk: Update 2.11.2 → 3.0.1
|
2023-06-26 15:51:40 -07:00 |
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p5-AcePerl
|
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p5-Bio-ASN1-EntrezGene
|
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
|
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p5-Bio-DB-EMBL
|
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p5-Bio-DB-NCBIHelper
|
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 |
|
p5-BioPerl-Run
|
|
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p5-transdecoder
|
p5-transdecoder: Update to 5.7.1
|
2023-08-05 15:58:40 -05:00 |
|
p5-TrimGalore
|
biology/p5-TrimGalore: Fix build
|
2023-08-05 22:05:05 +02:00 |
|
paml
|
biology/paml: Update to 4.10.7
|
2023-07-08 00:46:53 -03:00 |
|
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: Update to 1.88
|
2023-09-10 08:06:18 -05:00 |
|
primer3
|
biology/primer3: Fix build with llvm16
|
2023-08-05 20:55:50 +02:00 |
|
prodigal
|
biology/prodigal: Update 2.6.3-7 → 2.6.3-16
|
2023-07-22 00:37:33 -07:00 |
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prodigy-lig
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
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
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-biopython
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-biosig
|
*/*: Update WWW to use HTTPS for sourceforge.net projects
|
2023-11-06 11:03:47 +01:00 |
|
py-bx-python
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-crossmap
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-cutadapt
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-deeptools
|
biology/py-deeptools: Update to 3.5.2
|
2023-06-19 07:09:17 -05:00 |
|
py-deeptoolsintervals
|
|
|
|
py-dna-features-viewer
|
biology/py-dna-features-viewer: Update to 3.1.3
|
2023-11-04 17:11:34 -05:00 |
|
py-dnaio
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-ete3
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-Genesis-PyAPI
|
biology/py-Genesis-PyAPI: Add NO_ARCH
|
2023-08-01 00:42:07 +08:00 |
|
py-gffutils
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-goatools
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-gtfparse
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-hits
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-htseq
|
biology/py-htseq: Fix build with python-3.11
|
2024-01-21 07:13:35 +00:00 |
|
py-libnuml
|
|
|
|
py-libsedml
|
|
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py-loompy
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-macs2
|
biology/py-macs2: Update to 2.2.9.1
|
2023-08-06 13:17:52 -05:00 |
|
py-macs3
|
biology/py-macs3: Peak caller for TF binding sites
|
2024-01-10 09:19:56 -06:00 |
|
py-mrcfile
|
biology/py-mrcfile: update 1.4.3 → 1.5.0
|
2024-01-19 23:47:54 -08:00 |
|
py-multiqc
|
biology/py-multiqc: Update to 1.15
|
2023-08-05 11:18:37 -05:00 |
|
py-ont-fast5-api
|
|
|
|
py-orange3-bioinformatics
|
biology/py-orange3-bioinformatics: Change RUN_DEPENDS from py-requests-cache to py-requests-cache0
|
2023-08-01 00:42:07 +08:00 |
|
py-orange3-single-cell
|
biology/py-orange3-single-cell: Add NO_ARCH
|
2023-08-01 00:42:07 +08:00 |
|
py-pandas-charm
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
py-py2bit
|
|
|
|
py-pybigwig
|
biology/py-pybigwig: Update to 0.3.22
|
2023-12-16 07:59:37 -06:00 |
|
py-pyfaidx
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
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
|
|
|
|
py-resdk
|
biology/py-resdk: relax chardet limitation
|
2023-12-08 21:55:13 +01:00 |
|
py-scikit-bio
|
biology/py-scikit-bio: Update 0.5.8 → 0.5.9
|
2023-08-03 00:02:05 -07:00 |
|
py-valerius
|
|
|
|
py-xenaPython
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
pyfasta
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
python-nexus
|
all: remove explicit versions in USES=python for "3.x+"
|
2023-06-27 21:34:34 +02:00 |
|
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 |
|
rainbow
|
|
|
|
rampler
|
|
|
|
readseq
|
|
|
|
rna-seq
|
biology/rna-seq: Add biology/star dep to metaport
|
2023-07-31 09:36:06 -05:00 |
|
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
|
|
|
|
rubygem-bio-shell
|
|
|
|
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
|
biology/seqan-apps: Fix build with llvm16
|
2023-08-06 23:53:04 +02:00 |
|
seqkit
|
all: Bump PORTREVISION after lang/go* update
|
2023-12-07 02:22:10 +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
|
biology/sra-tools: Update to 3.0.6
|
2023-08-10 12:17:24 -05:00 |
|
stacks
|
|
|
|
star
|
biology/star: Fix SIMD issue on non-amd64
|
2023-08-21 09:33:20 -05:00 |
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
taxonkit
|
biology/taxonkit: update 0.15.0 → 0.15.1
|
2023-12-19 23:02:18 -08:00 |
|
treekin
|
*/*: chase the upgrade of BLAS / LAPACK to 3.12.0
|
2024-01-01 12:49:51 +01:00 |
|
treepuzzle
|
|
|
|
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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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
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MAN?PREFIX: eleminate its usage and move man to share/man
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2024-01-10 09:16:01 +01:00 |
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unikmer
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all: Bump 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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biology/vcftools: Unbreak build with clang 16
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2023-07-15 20:29:00 -05:00 |
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velvet
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viennarna
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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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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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*/*: Fix build with llvm16 on 13.2-STABLE
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2023-07-26 02:48:20 +02:00 |
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Makefile
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biology/recombine: Remove expired port
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2024-01-18 22:23:16 +01:00 |
