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abyss
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biology/abyss: Update 2.3.5 → 2.3.7
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2023-07-22 01:55:01 -07:00 |
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ad2vcf
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artemis
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atac-seq
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biology/atac-seq: Add curl to metaport deps
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2023-07-28 09:35:04 -05:00 |
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augustus
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biology/augustus: Fix build with llvm16
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2023-08-06 23:53:03 +02:00 |
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avida
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babel
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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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bfc
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bifrost
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biology/bifrost: Control -march via CPUTYPE make variable
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2023-08-12 09:38:47 -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: Update to 0.2.5
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2023-08-11 15:35:11 -05:00 |
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biolibc-tools
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biology/biolibc-tools: Update to 0.1.4.9
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2023-08-11 15:40:49 -05:00 |
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bioparser
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biosig
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biology/{,py-}biosig: Update 2.5.0 → 2.5.2
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2023-07-19 01:17:37 -07:00 |
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biosoup
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biology/biosoup: Update 0.10.0-2 → 0.11.0
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2023-05-19 00:54:16 -07:00 |
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biostar-tools
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bolt-lmm
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bowtie
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bowtie2
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btllib
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biology/btllib: New port: Bioinformatics Technology Lab common code library
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2023-07-21 15:24:04 -07:00 |
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bwa
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canu
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biology/canu: Fix build with llvm16
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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
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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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biology/chip-seq: Metaport for ChIP-Seq analysis
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2023-06-14 16:23:37 -05:00 |
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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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cytoscape
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ddocent
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diamond
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biology/diamond: Update to 2.1.8
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2023-07-08 00:45:48 -03:00 |
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dsr-pdb
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edlib
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emboss
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erminej
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exonerate
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fasda
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biology/fasda: Update to 0.1.4
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2023-08-11 15:39:06 -05:00 |
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fasta
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fasta3
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fastahack
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fastdnaml
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fastool
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fastp
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biology/fastp: Update to 0.23.4
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2023-05-31 10:40:00 -05:00 |
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fastq-trim
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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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biology/gatk: Update 4.3.0.0 → 4.4.0.0
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2023-06-04 15:02:58 -07:00 |
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gcta
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gemma
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generand
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gff2ps
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biology/gff2ps: drop maintainership
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2023-05-21 16:20:36 +00:00 |
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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+"
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2023-06-27 21:34:34 +02:00 |
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haplohseq
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biology/haplohseq: Fix build on FreeBSD 14
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2023-07-09 11:37:39 -05:00 |
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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+"
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2023-06-27 21:34:34 +02:00 |
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htslib
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hyphy
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biology/hyphy: Update to 2.5.52
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2023-08-09 14:39:17 -03:00 |
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igv
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infernal
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all: remove explicit versions in USES=python for "3.x+"
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2023-06-27 21:34:34 +02:00 |
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iolib
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iqtree
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jalview
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biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1
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2023-06-18 02:58:53 -07:00 |
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jellyfish
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kallisto
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biology/kallisto: Clean up build
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2023-07-24 10:44:58 -05:00 |
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kmcp
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all: Bump PORTREVISION after lang/go{119,120} update
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2023-08-04 09:24:50 -05:00 |
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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: Update 0.4.6 → 0.4.7
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2023-07-17 00:09:00 -07:00 |
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libcombine
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biology/libcombine: Fix build with libsbml 5.20.0
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2023-05-27 12:24:05 +08:00 |
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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+"
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2023-06-27 21:34:34 +02:00 |
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libnuml
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libsbml
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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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libsedml
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biology/libsedml: Fix build with libsbml 5.20.0
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2023-05-27 12:24:05 +08:00 |
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linux-foldingathome
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locarna
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biology/locarna: Fix tests
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2023-07-17 09:22:42 -07:00 |
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mafft
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mapm3
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mashmap
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biology/mashmap: Broken on i386; Fix build on other architectures by using NATIVE option
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2023-07-19 11:26:06 -07:00 |
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megahit
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metaeuk
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biology/metaeuk: Add NATIVE option
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2023-07-14 17:31:14 -07:00 |
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migrate
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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: Fix build on 14
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2023-08-18 08:57:12 +02:00 |
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mrbayes
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mummer
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muscle
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ncbi-blast+
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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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ncbi-cxx-toolkit
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graphics/proj: Update to 9.2.1
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2023-07-26 21:58:55 +02:00 |
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ncbi-entrez-direct
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all: Bump PORTREVISION after lang/go{119,120} update
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2023-08-04 09:24:50 -05:00 |
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ncbi-toolkit
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*/*: Bump jpeg-turbo users treewide
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2023-07-28 19:13:17 +02:00 |
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ncbi-vdb
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ngs-sdk
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biology/ngs-sdk: Update 2.11.2 → 3.0.1
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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
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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p5-BioPerl-Run
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p5-transdecoder
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p5-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: Fix build
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2023-08-05 22:05:05 +02:00 |
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paml
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biology/paml: Update to 4.10.7
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2023-07-08 00:46:53 -03:00 |
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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 0.1.4.11
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2023-08-11 15:44:14 -05:00 |
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pear-merger
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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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pooler
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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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biology/prodigal: Update 2.6.3-7 → 2.6.3-16
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2023-07-22 00:37:33 -07:00 |
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prodigy-lig
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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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protomol
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*/*: Bump jpeg-turbo users treewide
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2023-07-28 19:13:17 +02:00 |
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psi88
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py-bcbio-gff
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py-biom-format
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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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py-biopython
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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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py-biosig
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biology/{,py-}biosig: Update 2.5.0 → 2.5.2
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2023-07-19 01:17:37 -07:00 |
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py-bx-python
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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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py-crossmap
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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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py-cutadapt
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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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py-deeptools
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biology/py-deeptools: Update to 3.5.2
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2023-06-19 07:09:17 -05:00 |
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py-deeptoolsintervals
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py-dna-features-viewer
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py-dnaio
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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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py-ete3
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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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py-Genesis-PyAPI
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biology/py-Genesis-PyAPI: Add NO_ARCH
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2023-08-01 00:42:07 +08:00 |
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py-gffutils
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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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py-goatools
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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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py-gtfparse
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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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py-hits
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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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py-htseq
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biology/py-htseq: Update to 2.0.4
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2023-08-05 11:40:26 -05:00 |
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py-libnuml
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py-libsedml
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py-loompy
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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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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-mrcfile
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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-ont-fast5-api
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py-orange3-bioinformatics
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biology/py-orange3-bioinformatics: Change RUN_DEPENDS from py-requests-cache to py-requests-cache0
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2023-08-01 00:42:07 +08:00 |
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py-orange3-single-cell
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biology/py-orange3-single-cell: Add NO_ARCH
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2023-08-01 00:42:07 +08:00 |
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py-pandas-charm
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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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py-py2bit
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py-pybigwig
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py-pyfaidx
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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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py-pyrodigal
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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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py-pysam
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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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py-PySCeS
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biology/py-PySCeS: Update 1.1.0 → 1.1.1
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2023-07-25 23:20:25 -07:00 |
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py-python-libsbml
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biology/py-python-libsbml: Use CMAKE_BUILD_PARALLEL_LEVEL env var for parallelization
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2023-07-26 00:04:04 -07:00 |
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py-pywgsim
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py-resdk
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devel/py-setuptools: convert individual consumers to ${PY_SETUPTOOLS}
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2023-07-17 20:53:09 -04:00 |
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py-scikit-bio
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biology/py-scikit-bio: Update 0.5.8 → 0.5.9
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2023-08-03 00:02:05 -07:00 |
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py-valerius
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py-xenaPython
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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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pyfasta
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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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python-nexus
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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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rainbow
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rampler
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readseq
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recombine
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rna-seq
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biology/rna-seq: Add biology/star dep to metaport
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2023-07-31 09:36:06 -05:00 |
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ruby-bio
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rubygem-bio
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rubygem-bio-executables
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rubygem-bio-old-biofetch-emulator
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rubygem-bio-shell
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salmon
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devel/onetbb: Update to 2021.10.0
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2023-08-21 12:09:23 +02:00 |
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sam2pairwise
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samtools
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scrm
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seaview
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*/*: Bump jpeg-turbo users treewide
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2023-07-28 19:13:17 +02:00 |
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seqan
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seqan1
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seqan3
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seqan-apps
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biology/seqan-apps: Fix build with llvm16
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2023-08-06 23:53:04 +02:00 |
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seqio
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seqkit
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biology/seqkit: Update 2.5.0 → 2.5.1
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2023-08-08 22:52:28 -07:00 |
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seqtk
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biology/seqtk: Update to 1.4
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2023-05-23 17:42:13 -05:00 |
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seqwish
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biology/seqwish: Broken on i386
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2023-08-16 22:27:09 -07:00 |
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sigviewer
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sim4
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slclust
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smithwaterman
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snpeff
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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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spoa
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sra-tools
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biology/sra-tools: Update to 3.0.6
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2023-08-10 12:17:24 -05:00 |
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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 PORTREVISION after lang/go{119,120} update
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2023-08-04 09:24:50 -05:00 |
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treekin
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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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tRNAscan-SE
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ucsc-userapps
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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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ugene
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unikmer
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all: Bump PORTREVISION after lang/go{119,120} update
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2023-08-04 09:24:50 -05:00 |
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vcf2hap
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vcf-split
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vcflib
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biology/vcflib: not for armv6/7
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2023-07-31 01:59:09 +03:00 |
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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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biology/viennarna: Mark BROKEN on 14
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2023-08-18 08:57:13 +02:00 |
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vsearch
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biology/vsearch: Update to 2.23.0
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2023-07-08 14:10:45 -05:00 |
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vt
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wfa2-lib
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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/py-htseq: Python library for sequence analysis
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2023-07-28 10:41:58 -05:00 |
0e8f22496e