| .. |
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abyss
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Mk/bsd.commands.mk: Use absolute path to define GMAKE
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2024-12-29 12:34:56 +01:00 |
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ad2vcf
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andi
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biology/andi: New ports: Efficient estimation of evolutionary distances
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2024-09-07 14:31:10 -07:00 |
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artemis
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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atac-seq
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all: remove support for expired FreeBSD 13.3
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2025-01-01 17:09:59 +01:00 |
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augustus
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devel/boost: bump consumers after Boost-1.87 update
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2025-02-14 06:17:22 +03:00 |
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avida
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babel
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bamtools
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*/*: Bump dependencioes after devel/jsoncpp update
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2024-09-12 09:20:06 -07:00 |
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bamutil
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barrnap
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bbmap
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biology/bbmap: Update to 39.15
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2025-01-16 06:35:49 -06:00 |
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bcf-score
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*/*: bump PORTREVISION after the upgrade to Suitesparse
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2025-01-11 11:02:35 +01:00 |
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bcftools
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biology/bcftools: Update to 1.21
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2024-10-09 17:23:09 -05:00 |
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bedtools
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bfc
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bifrost
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bio-mocha
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biology/bio-mocha: Update to 1.20
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2024-10-09 17:23:10 -05:00 |
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bioawk
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biococoa
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biolibc
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biolibc-tools
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bioparser
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biosig
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*/*: bump PORTREVISION after the upgrade to Suitesparse
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2025-01-11 11:02:35 +01:00 |
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biosoup
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biostar-tools
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biology/biostar-tools: Update to 2.0
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2024-11-07 18:44:28 -06:00 |
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bolt-lmm
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*/*: Bump PORTREVISION after math/nlopt update
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2025-03-01 16:09:11 +01:00 |
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bowtie
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bowtie2
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btllib
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biology/btllib: update 1.7.3 → 1.7.5
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2024-12-05 10:11:11 -08:00 |
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bwa
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biology/bwa: update 0.7.18 => 0.7.19
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2025-03-26 08:34:34 +01:00 |
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canu
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devel/boost: bump consumers after Boost-1.87 update
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2025-02-14 06:17:22 +03:00 |
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cd-hit
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cdbfasta
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checkm
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biology/checkm: expire on 2025-06-01 for science/py-DendroPy
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2025-03-31 22:45:34 +02:00 |
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chip-seq
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clustal-omega
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clustalw
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coverm
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lang/rust: Bump revisions after 1.86.0
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2025-04-08 10:41:13 +02:00 |
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cufflinks
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devel/boost: bump consumers after Boost-1.87 update
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2025-02-14 06:17:22 +03:00 |
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cytoscape
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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ddocent
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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diamond
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biology/diamond: Update to 2.1.11
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2025-01-25 10:35:27 -04:00 |
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dsr-pdb
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devel/boost: bump consumers after Boost-1.87 update
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2025-02-14 06:17:22 +03:00 |
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edlib
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emboss
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erminej
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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exonerate
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biology/exonerate: remove maintainer (email address gone)
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2024-10-28 13:41:54 +01:00 |
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fasda
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fasda-utils
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biology/fasda-utils: Fast and simple differential analysis extras
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2025-04-06 06:27:20 -05:00 |
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fasta
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fasta3
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fastahack
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fastani
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biology/fastani: Broken where OpenMP isn't available; Update WWW
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2024-11-02 23:47:52 -07:00 |
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fastdnaml
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fastool
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fastp
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biology/fastp: Update to 0.24.1
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2025-04-17 07:51:42 -05:00 |
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fastq-trim
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fastqc
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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fasttree
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biology/fasttree: Update to 2.1.11
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2024-12-03 08:55:06 -06:00 |
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fastx-toolkit
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fermi-lite
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biology/fermi-lite: enable on powerpc64le
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2025-01-29 17:56:29 +01:00 |
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figtree
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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flash
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fluctuate
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freebayes
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biology/freebayes: Update to 1.3.9
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2025-02-18 14:45:11 -06:00 |
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garlic
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gatk
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biology/gatk: Update WWW
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2025-02-14 02:30:52 -08:00 |
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gcta
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*/*: bump PORTREVISION after OpenBLAS upgrade
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2025-01-28 17:42:55 +01:00 |
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gemma
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*/*: bump PORTREVISION after OpenBLAS upgrade
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2025-01-28 17:42:55 +01:00 |
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generand
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gff2ps
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gffread
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gkl
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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gmap
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gperiodic
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gnome.mk: rename gdkpixbuf2 to gdkpixbuf to prepare for port move
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2025-03-17 00:02:08 -04:00 |
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graphlan
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groopm
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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haplohseq
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biology/haplohseq: mark as BROKEN with Boost>=1.87 (+)
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2025-02-14 06:17:11 +03:00 |
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hhsuite
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hisat2
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hmmer
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biology/hmmer: update to 3.4
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2024-10-28 13:41:48 +01:00 |
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htslib
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biology/htslib: Update to 1.21
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2024-10-09 17:23:08 -05:00 |
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hyphy
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biology/hyphy: Update to 2.5.70
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2025-03-23 22:33:03 -03:00 |
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igv
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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infernal
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biology/infernal: update 1.1.4 → 1.1.5
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2025-01-30 08:35:31 +01:00 |
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iolib
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iqtree
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devel/boost: bump consumers after Boost-1.87 update
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2025-02-14 06:17:22 +03:00 |
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jalview
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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jellyfish
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kallisto
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biology/kallisto: Update to 0.51.1,1
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2024-09-19 17:46:47 -05:00 |
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kmcp
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go: Bump ports for go124 update
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2025-04-01 22:07:58 -04:00 |
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lamarc
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libbigwig
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biology/libbigwig: update 0.4.7 → 0.4.8
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2025-01-18 01:52:23 -08:00 |
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libcombine
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libgff
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libgtextutils
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libneurosim
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devel/automake: Update to 1.17
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2024-07-20 13:27:02 +02:00 |
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libnuml
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biology/{,py-}libnuml: update 1.1.6 → 1.1.7
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2025-03-28 02:54:11 -07:00 |
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libsbml
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textproc/xerces-c3: Update to 3.3.0
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2024-10-25 23:56:41 +08:00 |
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libsedml
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linux-foldingathome
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biology/linux-foldingathome: Update to 8.4.9.
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2025-02-14 09:21:35 +01:00 |
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locarna
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mafft
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mapm3
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mashmap
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mca-calling
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biology/mca-calling: Core tools for mCA event calling
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2024-10-24 08:32:05 -05:00 |
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megahit
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metaeuk
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biology/metaeuk: builds now fine on powerpc64le
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2025-01-29 17:56:26 +01:00 |
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migrate
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biology/migrate: fix build on !x86
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2024-07-09 12:04:31 +02:00 |
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minimap2
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biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors
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2024-07-20 14:55:08 -05:00 |
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mmseqs2
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biology/mmseqs2: Update to 17.b804.f
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2025-01-25 07:24:31 -06:00 |
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molden
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all: return jmd's ports to the pool after safekeeping their commit bit.
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2024-11-28 17:10:52 +01:00 |
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mothur
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biology/mothur: update 1.48.1 → 1.48.2
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2024-11-04 23:25:49 -08:00 |
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mrbayes
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mummer
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biology/mummer: update 4.0.0 → 4.0.1
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2025-02-08 00:07:06 -08:00 |
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muscle
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ncbi-blast+
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biology/ncbi-blast+: Update to 2.16.0_3
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2025-03-06 06:42:48 -06:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: Broken on i386
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2025-03-10 01:13:13 -07:00 |
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ncbi-entrez-direct
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go: Bump ports for go124 update
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2025-04-01 22:07:58 -04:00 |
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ncbi-toolkit
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all: drop support for expired FreeBSD 14.0
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2024-10-01 20:56:20 +02:00 |
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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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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-TrimGalore
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biology/p5-TrimGalore: Update to 0.6.10
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2024-07-23 11:01:28 -04:00 |
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paml
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pbbam
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devel/boost: bump consumers after Boost-1.87 update
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2025-02-14 06:17:22 +03:00 |
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peak-classifier
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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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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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plink
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*/*: bump PORTREVISION after OpenBLAS upgrade
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2025-01-28 17:42:55 +01:00 |
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pooler
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biology/pooler: Update to 1.89
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2025-02-01 01:36:31 +00:00 |
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preseq
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preseq: Not for 32-bit platforms
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2024-11-24 07:50:11 -06:00 |
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primer3
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prodigal
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prodigy-lig
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biology/prodigy-lig: update 1.1.2 → 1.1.3
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2024-10-15 08:33:52 -07:00 |
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protomol
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psi88
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py-bcbio-gff
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-biom-format
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-biopython
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-biosig
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-bx-python
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Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
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2025-04-09 22:55:11 +08:00 |
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py-crossmap
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-cutadapt
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-deeptools
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-deeptoolsintervals
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-dna-features-viewer
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-dnaio
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Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
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2025-04-09 22:55:11 +08:00 |
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py-ete3
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-Genesis-PyAPI
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-gffutils
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-goatools
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-gtfparse
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biology/py-gtfparse: Fix fetch
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2024-12-05 19:44:23 -08:00 |
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py-hits
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-htseq
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-libnuml
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biology/{,py-}libnuml: update 1.1.6 → 1.1.7
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2025-03-28 02:54:11 -07:00 |
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py-libsedml
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py-loompy
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-macs2
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-macs3
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Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
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2025-04-09 22:55:11 +08:00 |
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py-mrcfile
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-multiqc
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-newick
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biology/py-newick: Update to 1.10.0
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2025-03-22 13:41:03 +00:00 |
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py-ont-fast5-api
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-orange3-bioinformatics
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-orange3-single-cell
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biology/py-orange3-single-cell: expire on 2025-06-01 for math/py-fastdtw
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2025-03-31 16:19:33 +02:00 |
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py-pandas-charm
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-py2bit
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-pybigwig
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-pyfaidx
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
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2025-03-07 23:05:21 -05:00 |
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py-pyrodigal
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Mk/Uses/python.mk: Introduce USE_PYTHON=cython3{,_run,_test}
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2025-04-09 22:55:11 +08:00 |
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py-pysam
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-PySCeS
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biology/py-PySCeS: update 1.2.1 → 1.2.2
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2024-08-03 01:27:31 -07:00 |
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py-python-libsbml
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-pywgsim
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-resdk
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biology/py-resdk: update 21.2.1 → 22.0.0
|
2025-04-02 02:10:43 -07:00 |
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py-scikit-bio
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biology/py-scikit-bio: update 0.6.2 → 0.6.3
|
2025-01-13 19:26:05 -08:00 |
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py-valerius
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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py-xenaPython
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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pyfasta
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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python-nexus
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python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
|
2025-03-07 23:05:21 -05:00 |
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R-cran-Biobase
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biology/R-cran-Biobase: Update to 2.66.0
|
2025-04-11 14:28:35 +00:00 |
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R-cran-BiocGenerics
|
biology/R-cran-BiocGenerics: Update to 0.52.0
|
2025-04-11 14:28:35 +00:00 |
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R-cran-BiocManager
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biology/R-cran-BiocManager: Update version 1.30.24=>1.30.25
|
2024-09-08 19:28:55 +02:00 |
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rainbow
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rampler
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readseq
|
Mk/**java.mk: Convert bsd.java.mk to USES
|
2024-12-31 09:57:55 +01:00 |
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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 2.0.6
|
2025-03-19 11:46:26 +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/boost: bump consumers after Boost-1.87 update
|
2025-02-14 06:17:22 +03:00 |
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sam2pairwise
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samtools
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biology/samtools: Update to 1.21
|
2024-10-09 17:23:09 -05:00 |
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scrm
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seaview
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biology/seaview: Update version 5.0.5=>5.1
|
2025-03-26 08:36:45 +01:00 |
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seqan
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seqan-apps
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seqan1
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seqan3
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seqkit
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go: Bump ports for go124 update
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2025-04-01 22:07:58 -04:00 |
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seqtk
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seqwish
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biology/seqwish: Set OPENMP=OFF and broken where OpenMP isn't available
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2025-02-23 11:42:19 -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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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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spoa
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sra-tools
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biology/sra-tools: Update to 3.2.1
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2025-03-21 06:27:22 -05:00 |
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stacks
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biology/stacks: fix build without libomp
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2025-01-22 12:27:04 +01:00 |
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star
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stringtie
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subread
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biology/subread: Update to 2.1.0
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2025-03-27 17:05:26 -05:00 |
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tabixpp
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biology/tabixpp: Undeprecate and update to 1.1.2
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2025-02-18 09:39:35 -06:00 |
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taxonkit
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go: Bump ports for go124 update
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2025-04-01 22:07:58 -04:00 |
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treekin
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*/*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS
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2025-01-24 13:18:28 +01:00 |
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treepuzzle
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trimadap
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biology/trimadap: drop not necessary powerpc64le knob
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2025-01-29 17:56:25 +01:00 |
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trimmomatic
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Mk/**java.mk: Convert bsd.java.mk to USES
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2024-12-31 09:57:55 +01:00 |
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tRNAscan-SE
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ucsc-userapps
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biology/ucsc-userapps: Update to v474
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2024-11-28 09:59:20 -06:00 |
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ugene
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unikmer
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go: Bump ports for go124 update
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2025-04-01 22:07:58 -04:00 |
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vcf-split
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vcf2hap
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vcflib
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biology/vcflib: Update to 1.0.12
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2024-11-25 08:49:37 -06:00 |
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vcftools
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velvet
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viennarna
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*/*: bump PORTREVISION to chase blas/lapack, Suitesparse and BLIS
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2025-01-24 13:18:28 +01:00 |
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vsearch
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biology/vsearch: Update to 2.30.0
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2025-03-02 06:37:09 -06:00 |
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vt
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wfa2-lib
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biology/wfa2-lib: fix build without libomp
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2024-08-04 14:00:47 +02:00 |
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wise
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all: drop support for expired FreeBSD 14.0
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2024-10-01 20:56:20 +02:00 |
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Makefile
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biology/fasda-utils: Fast and simple differential analysis extras
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2025-04-06 06:27:20 -05:00 |
b3f6f8596d