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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 0.1.5
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2022-03-15 16:39:32 -05:00 |
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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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Fix CONFLICTS entries of multiple ports
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2022-01-10 16:15:39 +01:00 |
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bbmap
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biology/bbmap: Update to 38.92
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2021-08-22 08:59:58 -05:00 |
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bcftools
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biology/bcftools: Update to 1.15
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2022-02-26 09:04:10 -06:00 |
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bedtools
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bfc
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biology/bfc: Correct sequencing errors from Illumina sequencing data
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2021-08-23 12:28:41 -05:00 |
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bio-mocha
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biology/bio-mocha: Update bcftools submodule to 1.15
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2022-02-26 09:04:10 -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 0.2.2
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2022-03-15 16:35:22 -05:00 |
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biolibc-tools
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biology/biolibc-tools: Update to 0.1.2
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2022-03-15 16:36:49 -05:00 |
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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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biology/biosig: Update 2.3.3 -> 2.4.0
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2022-03-20 12:43:56 -07:00 |
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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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biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64
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2022-04-21 17:11:13 +00:00 |
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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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biology/bowtie2: Update to 2.4.5
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2022-01-21 08:33:54 -06:00 |
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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: check for omp.h on all architectures
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2022-04-27 13:22:07 +00:00 |
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cdbfasta
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checkm
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biology/checkm: Update 1.1.10 -> 1.1.11
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2022-04-25 13:50:10 -07:00 |
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clustal-omega
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clustalw
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cufflinks
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Fix CONFLICTS entries of multiple ports
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2022-01-10 16:15:39 +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 2.0.15
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2022-04-24 14:50:21 -03:00 |
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dsr-pdb
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biology/dsr-pdb: Remove -pg (mcount instrumentation) flag
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2022-03-21 17:07:11 -07:00 |
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edlib
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biology/edlib: Update 1.2.6.20201202 -> 1.2.7
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2021-08-21 10:12:15 -07:00 |
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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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biology/erminej: Analyses of gene sets, e.g. gene expression profiling
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2021-07-09 07:26:58 -05:00 |
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exonerate
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fasta
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Fix CONFLICTS entries of multiple ports
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2022-01-10 16:15:39 +01:00 |
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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: Add USE_GCC to hack around seg faults
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2022-01-21 10:16:01 -06:00 |
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fastq-trim
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biology/fastq-trim: Update to 0.1.1.4
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2022-03-21 16:19:36 -05:00 |
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fastqc
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fasttree
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biology/fasttree: check for omp.h on all architectures
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2022-04-27 13:22:02 +00:00 |
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fastx-toolkit
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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figtree
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flash
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biology/flash: Fast Length Adjustment of SHort reads
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2021-08-23 12:26:47 -05:00 |
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fluctuate
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freebayes
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biology/freebayes: Update to 1.3.6
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2022-02-06 14:23:45 -06:00 |
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garlic
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gatk
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biology/gatk: Update 4.2.0.0 -> 4.2.6.0
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2022-04-10 16:21:50 -07:00 |
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gcta
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gemma
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math/gsl: bump portrevision of consumers after update to 2.7.1
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2022-01-12 20:41:22 +01:00 |
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generand
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gff2ps
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gffread
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biology/gffread: remove local poudriere files
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2022-03-07 23:44:38 +01:00 |
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gmap
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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gperiodic
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graphlan
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groopm
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biology/groopm: Fix build with setuptools 58.0.0+
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2022-03-25 21:38:04 +08:00 |
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haplohseq
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hhsuite
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biology/hhsuite: check for omp.h on all architectures
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2022-04-27 13:22:04 +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 1.15
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2022-02-26 09:04:10 -06:00 |
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hyphy
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biology/hyphy: Update to 2.5.38
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2022-04-24 15:24:30 -03:00 |
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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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*/*: fix trailing whitespace in pkg-descr's
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2022-04-01 18:09:49 +03:00 |
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iolib
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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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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biology/kallisto: Update to 0.48.0
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2022-01-19 07:57:36 -06:00 |
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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/{,py-}libnuml: Update 1.1.5 -> 1.1.6
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2022-04-23 18:36:56 -07:00 |
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libsbml
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textproc/libxml2: bump all LIB_DEPENDS consumers
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2022-04-10 15:11:41 -04:00 |
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libsedml
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biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31
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2022-04-22 11:04:38 -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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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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minimap2
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biology/minimap2: Update to 2.24
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2021-12-31 08:30:52 -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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*: Clean up some things
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2022-01-17 14:20:25 +01:00 |
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mopac
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mothur
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biology/mothur: Update 1.46.1 -> 1.47.0
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2022-01-21 09:14:38 -08:00 |
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mrbayes
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mummer
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Fix CONFLICTS entries of multiple ports
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2022-01-10 16:15:39 +01:00 |
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muscle
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ncbi-blast+
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biology/ncbi-blast+: check for omp.h on all architectures
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2022-04-27 13:22:09 +00:00 |
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ncbi-cxx-toolkit
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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ncbi-entrez-direct
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*/*: Bump PORTREVISION after lang/go 1.18 update
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2022-03-30 03:01:44 -04:00 |
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ncbi-toolkit
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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ncbi-vdb
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textproc/libxml2: bump all LIB_DEPENDS consumers
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2022-04-10 15:11:41 -04:00 |
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ngs-sdk
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biology/ngs-sdk: Update 2.11.1 -> 2.11.2
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2022-01-27 01:29:09 -08:00 |
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7
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2021-07-06 22:56:10 +08:00 |
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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p5-BioPerl
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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 0.1.3
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2022-03-15 16:41:51 -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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biology/phyml: update to 3.3.20211231
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2022-01-02 18:31:24 +01:00 |
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picard-tools
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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plink
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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pooler
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biology/pooler: use openmp only when omp.h is present
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2022-04-27 13:22:12 +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-bcbio-gff
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biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)
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2022-02-03 13:38:42 -06:00 |
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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: Fix build with setuptools 58.0.0+
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2022-03-25 21:38:04 +08:00 |
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py-cutadapt
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biology/py-cutadapt: fix tests by adding missing test depend
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2022-04-07 21:59:32 +03:00 |
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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-dna-features-viewer
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biology/py-dna-features-viewer: Add missing dependency
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2022-02-12 09:12:39 -06:00 |
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py-dnaio
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py-ete3
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devel/py-qt5, devel/py-sip: Update versions
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2022-03-07 18:39:13 +01:00 |
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py-Genesis-PyAPI
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py-gffutils
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py-goatools
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biology/py-goatools: Tools for processing and visualizing Gene Ontology terms
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2021-07-02 12:00:29 -05:00 |
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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: Update 1.1.5 -> 1.1.6
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2022-04-23 18:36:56 -07:00 |
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py-libsedml
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biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31
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2022-04-22 11:04:38 -07:00 |
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py-loompy
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biology/py-loompy: Update 3.0.6 -> 3.0.7
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2022-03-06 09:09:59 -08:00 |
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py-macs2
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py-multiqc
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py-ont-fast5-api
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biology/py-ont-fast5-api: Update to 4.0.2
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2022-03-25 11:37:29 -05:00 |
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py-orange3-bioinformatics
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cleanup: remove transitive py27 deprecation (www/qt5-webengine)
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2022-01-23 21:56:25 +01:00 |
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py-orange3-single-cell
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cleanup: remove transitive py27 deprecation (www/qt5-webengine)
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2022-01-23 21:56:25 +01:00 |
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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 0.18.0 -> 0.19.0
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2022-04-27 10:38:26 -07:00 |
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py-PySCeS
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biology/py-PySCeS: fix with Python ≠ 3.8
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2022-03-02 19:49:25 +01:00 |
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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 14.0.0 -> 14.1.0
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2022-04-27 10:38:25 -07:00 |
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py-scikit-bio
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biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64
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2022-04-21 17:11:15 +00:00 |
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py-xenaPython
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pyfasta
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python-nexus
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biology/python-nexus: Fix build with setuptools 58.0.0+
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2022-03-25 21:38:05 +08:00 |
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rainbow
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rampler
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readseq
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recombine
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ruby-bio
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Fix CONFLICTS entries of multiple ports
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2022-01-10 16:15:39 +01:00 |
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rubygem-bio
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biology/rubygem-bio: Update to 2.0.3
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2022-01-12 02:47:28 +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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Fix CONFLICTS entries of multiple ports
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2022-01-10 16:15:39 +01:00 |
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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 1.15
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2022-02-26 09:04:10 -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
|
2021-10-29 11:50:18 +02:00 |
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seqan1
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Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
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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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biology/seqan-apps: remove obsolete USE_GCC
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2022-04-25 14:12:52 +00:00 |
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seqio
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seqkit
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biology/seqkit: Update 2.1.0 -> 2.2.0
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2022-04-19 20:44:55 -07:00 |
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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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misc/: Update 0.99.6-2 -> 0.991
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2021-08-18 10:17:45 -07:00 |
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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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devel/cpu_features: Install cmake files, install headers into a dedicated directory
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2022-01-26 08:45:29 -08:00 |
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sra-tools
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textproc/libxml2: bump all LIB_DEPENDS consumers
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2022-04-10 15:11:41 -04:00 |
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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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*/*: Bump PORTREVISION after lang/go 1.18 update
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2022-03-30 03:01:44 -04:00 |
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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.)
|
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 0.18.8 -> 0.19.0
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2022-04-26 11:51:57 -07:00 |
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vcf2hap
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biology/vcf2hap: Update to 0.1.5
|
2022-03-15 16:45:04 -05:00 |
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vcf-split
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biology/vcf-split: Update to 0.1.4
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2022-03-15 16:43:40 -05:00 |
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vcflib
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
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vcftools
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biology/vcftools: Add CPE information
|
2021-09-25 20:28:38 +00:00 |
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velvet
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viennarna
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Update CONFLICTS definitions in categories a* to c*
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2022-02-06 19:36:07 +01:00 |
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vsearch
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biology/vsearch: Update to 2.21.1
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2022-01-23 16:32:43 -06:00 |
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vt
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wise
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Makefile
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biology/fastq-trim: Lightening fast sequence read trimmer
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2022-03-19 07:25:58 -05:00 |
