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abyss
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cleanup: drop support for EOL FreeBSD 11.X
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2021-09-30 23:23:30 +02:00 |
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ad2vcf
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biology/ad2vcf: Update to 0.1.4
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2021-12-14 13:45:31 -06:00 |
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artemis
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avida
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babel
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*/*: Remove redundant '-*' from CONFLICTS definitions
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2021-11-25 22:40:11 +01:00 |
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bamtools
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devel/jsoncpp: Update to 1.9.4 -> 1.9.5
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2021-11-05 12:09:19 -07:00 |
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bamutil
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biology/bamutil: Update to 1.0.15
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2021-10-20 14:43:38 -05:00 |
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bbmap
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bcftools
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biology/bcftools: Update to 1.14
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2021-12-18 11:56:51 -06:00 |
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bedtools
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bfc
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bio-mocha
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bio-mocha: Build plugin against bcftools 1.14, the current port
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2021-12-21 10:17:11 -06:00 |
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bioawk
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biococoa
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biolibc
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biology/biolibc: Update to 0.2.1
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2021-12-14 13:45:31 -06:00 |
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biolibc-tools
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biology/biolibc-tools: Update to 0.1.1
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2021-12-14 13:45:32 -06:00 |
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bioparser
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biology/bioparser: Update 3.0.12-2 -> 3.0.15
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2021-09-21 09:41:49 -07:00 |
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biosig
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biosoup
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biostar-tools
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biology/biostar-tools: Allow package build on non-amd64 systems
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2021-12-01 09:49:28 -06:00 |
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bolt-lmm
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bowtie
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biology/bowtie: enable on riscv64
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2021-12-15 13:55:57 +01:00 |
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bowtie2
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bwa
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biology/bwa: don't use GCC on powerpc64le
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2021-12-01 17:34:18 +00:00 |
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canu
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biology/canu: fix CATEGORIES
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2021-12-20 12:59:13 +00:00 |
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cd-hit
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biology/cd-hit: fix build on armv7
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2021-11-21 13:26:44 +00:00 |
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cdbfasta
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checkm
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clustal-omega
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clustalw
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cufflinks
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devel/automake: update to 1.16.5
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2021-12-12 19:46:22 +01:00 |
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cytoscape
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ddocent
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cleanup: drop support for EOL FreeBSD 11.X
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2021-09-30 23:23:30 +02:00 |
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diamond
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biology/diamond: Update to 2.0.13
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2021-11-11 13:17:24 -04:00 |
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dsr-pdb
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edlib
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emboss
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*/*: Remove redundant '-[0-9]*' from CONFLICTS
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2021-10-29 11:50:18 +02:00 |
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erminej
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exonerate
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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 0.23.1
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2021-10-20 11:37:39 -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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biology/freebayes: enable on riscv64
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2021-12-17 14:26:57 +01:00 |
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garlic
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gatk
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gcta
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gemma
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generand
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gff2ps
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gffread
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biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc
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2021-11-10 14:49:10 -06:00 |
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gmap
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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gperiodic
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graphlan
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groopm
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haplohseq
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hhsuite
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biology/hhsuite: fix packaging on powerpc
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2021-11-16 12:03:42 +00:00 |
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hisat2
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biology/hisat2: enable on riscv64
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2021-12-16 22:38:56 +01:00 |
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hmmer
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htslib
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biology/htslib: Update to 1.14
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2021-12-18 11:56:50 -06:00 |
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hyphy
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biology/hyphy: Update to 2.5.33
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2021-11-17 07:51:41 -04:00 |
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igv
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cleanup: drop support for EOL FreeBSD 11.X
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2021-09-30 23:23:30 +02:00 |
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infernal
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iolib
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iqtree
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jalview
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cleanup: drop support for EOL FreeBSD 11.X
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2021-09-30 23:23:30 +02:00 |
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jellyfish
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*: Clean up some things
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2021-10-12 17:01:38 +02:00 |
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kallisto
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lamarc
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libbigwig
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libgff
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biology/libgff: GFF/GTF parsing library based on GCLib
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2021-12-05 14:50:42 -06:00 |
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libgtextutils
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libneurosim
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biology/libneurosim: New port: Common interfaces for neuronal simulators
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2021-10-08 10:20:27 -07:00 |
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libnuml
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biology/libnuml: New port: C++ library for Numerical Markup Language
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2021-09-18 23:47:02 -07:00 |
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libsbml
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biology/libsbml: Fix build with Python 3.10
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2021-11-02 05:28:40 +08:00 |
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libsedml
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biology/libsedml: New port: C++ SED-ML library
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2021-09-19 11:15:35 -07:00 |
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linux-foldingathome
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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mafft
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biology/mafft: Update to 7.267
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2021-10-22 13:11:23 +08:00 |
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mapm3
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migrate
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minimap2
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biology/minimap2: Unbreak on i386 by resotring -msse flags
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2021-12-03 11:22:37 -06:00 |
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mmseqs2
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biology/mmseqs2: disable on 32-bits
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2021-09-12 21:05:53 +00:00 |
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molden
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mopac
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mothur
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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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devel/grpc: Update to 1.42.0
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2021-12-22 02:46:21 +08:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0
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2021-10-01 00:14:37 -07:00 |
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ncbi-entrez-direct
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ncbi-toolkit
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ncbi-vdb
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ngs-sdk
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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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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paml
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pbbam
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*: fix tab vs. space issues, and comments according to the guide.
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2021-10-16 11:51:39 +02:00 |
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pbseqan
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*: fix tab vs. space issues, and comments according to the guide.
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2021-10-16 11:51:39 +02:00 |
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peak-classifier
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biology/peak-classifier: Update to 0.1.2
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2021-12-14 13:45:32 -06:00 |
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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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devel/automake: update to 1.16.5
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2021-12-12 19:46:22 +01:00 |
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picard-tools
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plink
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pooler
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biology/pooler: fix build on powerpc
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2021-10-06 20:52:30 +00:00 |
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primer3
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prodigal
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prodigy-lig
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protomol
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psi88
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py-biom-format
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py-biopython
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biology/py-biopython: Update to 1.79
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2021-10-12 14:43:04 +08:00 |
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py-bx-python
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biology/py-bx-python: Update 0.8.11-6 -> 0.8.13
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2021-12-21 01:03:57 -08:00 |
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py-crossmap
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biology/py-crossmap: chase ad5a0604c4
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2021-10-14 00:53:16 +00:00 |
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py-cutadapt
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py-deeptools
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biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
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2021-10-14 06:51:12 -05:00 |
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py-deeptoolsintervals
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biology/py-deeptoolsintervals: Python interface for deepTools interval trees
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2021-10-13 11:02:13 -05:00 |
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py-dnaio
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py-ete3
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py-Genesis-PyAPI
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py-gffutils
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py-goatools
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py-gtfparse
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py-hits
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py-libnuml
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biology/py-libnuml: fix install with python 3.10+
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2021-11-02 21:08:32 +03:00 |
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py-libsedml
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biology/py-libsedml: fix install with python 3.10+
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2021-11-02 21:08:31 +03:00 |
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py-loompy
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py-macs2
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py-multiqc
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py-ont-fast5-api
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py-orange3-bioinformatics
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py-orange3-single-cell
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py-pandas-charm
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py-py2bit
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biology/py-py2bit: Python interface for 2bit packed nucleotide files
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2021-10-13 07:53:53 -05:00 |
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py-pybigwig
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biology/py-bigwig: Rename to biology/py-pybigwig
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2021-10-13 16:21:32 -05:00 |
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py-pyfaidx
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py-pysam
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biology/py-pysam: Update 0.16.0.1 -> 0.18.0
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2021-12-19 23:48:52 -08:00 |
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py-PySCeS
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biology/py-PySCeS: Update 0.9.8a -> 1.0.0
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2021-09-20 14:34:22 -07:00 |
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py-python-libsbml
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biology/py-python-libsbml: limit supported python versions, fix build
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2021-11-03 21:26:41 +03:00 |
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py-pywgsim
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biology/py-pywgsim: Modified wgsim genomic data simulator
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2021-09-06 07:55:49 -05:00 |
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py-resdk
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biology/py-resdk: Update 13.6.0 -> 13.7.0
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2021-11-17 22:33:39 -08:00 |
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py-scikit-bio
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py-xenaPython
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pyfasta
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python-nexus
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rainbow
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rampler
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readseq
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recombine
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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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biology/rubygem-bio-shell: Update to 1.0.1
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2021-11-22 02:21:58 +08:00 |
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sam2pairwise
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biology/sam2pairwise: Show pairwise alignment for each read in a SAM file
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2021-09-07 15:32:29 -05:00 |
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samtools
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biology/samtools: Update to 1.14
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2021-12-18 11:56:51 -06:00 |
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scrm
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seaview
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biology/seaview: Update version 5.0.4=>5.0.5
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2021-12-05 19:02:42 -06:00 |
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seqan
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*/*: Remove redundant '-[0-9]*' from CONFLICTS
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2021-10-29 11:50:18 +02:00 |
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seqan1
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seqan3
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biology/seqan3: Update 3.0.3 -> 3.1.0
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2021-11-14 21:18:53 -08:00 |
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seqan-apps
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*/*: Remove compiler:openmp from Mk/Uses/compiler.mk
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2021-10-03 19:47:27 +02:00 |
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seqio
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seqkit
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biology/seqkit: Update 2.0.1 -> 2.1.0
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2021-11-16 10:57:47 -08:00 |
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seqtk
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biology/seqtk: Update to 1.3
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2021-12-18 13:37:06 -06:00 |
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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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spoa
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sra-tools
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stacks
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star
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biology/star: Update to 2.7.9a
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2021-11-26 15:57:02 -06:00 |
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stringtie
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subread
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tabixpp
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taxonkit
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biology/taxonkit: Update 0.8.0 -> 0.9.0
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2021-12-02 12:57:06 -08:00 |
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treekin
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biology/treekin: Unbreak
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2021-10-15 08:50:24 -07:00 |
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treepuzzle
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trimadap
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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trimmomatic
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tRNAscan-SE
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ucsc-userapps
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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ugene
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biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
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2021-10-14 11:23:37 +00:00 |
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unikmer
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biology/unikmer: Update 0.18.4 -> 0.18.8
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2021-09-26 01:54:07 -07:00 |
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vcf2hap
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biology/vcf2hap: Update to 0.1.4
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2021-12-14 13:45:32 -06:00 |
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vcf-split
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biology/vcf-split: Update to 0.1.3.3
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2021-12-14 13:45:32 -06:00 |
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vcflib
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biology/vcflib: unbreak on riscv64
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2021-12-16 22:49:25 +01:00 |
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vcftools
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biology/vcftools: Add CPE information
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2021-09-25 20:28:38 +00:00 |
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velvet
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viennarna
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vsearch
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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vt
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wise
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Makefile
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biology/libgff: GFF/GTF parsing library based on GCLib
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2021-12-05 14:50:42 -06:00 |
