| .. |
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abyss
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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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ad2vcf
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biology/ad2vcf: Update to 0.1.6
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2022-06-11 09:26:57 -05:00 |
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artemis
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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avida
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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babel
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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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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bcftools
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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bedtools
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bfc
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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 0.2.3
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2022-06-11 09:26:56 -05:00 |
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biolibc-tools
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*: bump PORTREVISION of all devel/xxhash users...
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2022-08-13 20:51:14 +02:00 |
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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 2.4.1 -> 2.4.2
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2022-06-19 09:53:42 -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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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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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: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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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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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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checkm
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biology/checkm: Update 1.1.11 -> 1.2.0
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2022-05-01 11:14:09 -07:00 |
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clustal-omega
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clustalw
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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cufflinks
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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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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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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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edlib
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emboss
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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erminej
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exonerate
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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fasta
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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fasta3
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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fastahack
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fastdnaml
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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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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biology/figtree: Update 1.4.4 -> 1.4.4-14
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2022-08-27 22:52:00 -07:00 |
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flash
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fluctuate
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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gatk
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biology/gatk: mark BROKEN
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2022-08-11 21:33:41 +03:00 |
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gcta
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biology/gcta: Use bundled version of eigen3
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2022-07-06 13:40:04 -07:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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gperiodic
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cleanup: remove '$MCom' tag
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2022-07-20 21:44:12 +02:00 |
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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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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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hhsuite
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biology/hhsuite: Fix build on some architectures
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2022-08-04 09:21:45 -07:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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htslib
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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hyphy
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biology/hyphy: Update 2.5.40 -> 2.5.41
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2022-08-06 15:23:11 -07:00 |
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igv
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cleanup: drop support for EOL FreeBSD 11.X
|
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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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iqtree
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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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jalview
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +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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science/hdf5: bump PORTREVISION of consumers
|
2022-07-20 16:35:24 +02:00 |
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kmcp
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biology/kmcp: Update 0.8.3 -> 0.8.4
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2022-08-18 11:56:49 -07:00 |
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lamarc
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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libbigwig
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libgff
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biology/libgff: GFF/GTF parsing library based on GCLib
|
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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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libsedml
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biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32
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2022-06-08 22:53:28 -07:00 |
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linux-foldingathome
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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mafft
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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mapm3
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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migrate
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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minimap2
|
biology/minimap2: Update to 2.24
|
2021-12-31 08:30:52 -06:00 |
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mmseqs2
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biology/mmseqs2: Not require OpenMP on systems where OpenMP isn't enabled
|
2022-07-23 09:40:43 -07:00 |
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molden
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biology/molden: Update 6.7 -> 7.1
|
2022-07-23 13:00:53 -07:00 |
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mothur
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biology/mothur: Update 1.47.0 -> 1.48.0
|
2022-05-19 19:10:18 -07:00 |
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mrbayes
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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mummer
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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muscle
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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ncbi-blast+
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devel/grpc: Update to 1.48.0
|
2022-07-30 13:57:09 +08:00 |
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ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Broken on armv6
|
2022-08-06 16:28:43 -07:00 |
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ncbi-entrez-direct
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all: Bump PORTREVISION after Go update
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2022-08-03 16:35:13 -05:00 |
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ncbi-toolkit
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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ncbi-vdb
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science/hdf5: bump PORTREVISION of consumers
|
2022-07-20 16:35:24 +02:00 |
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ngs-sdk
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biology/ngs-sdk: Broken on armv6, armv7
|
2022-07-22 15:34:07 -07:00 |
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p5-AcePerl
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-ASN1-EntrezGene
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Cluster
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Coordinate
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Das
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Das-Lite
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-DB-EMBL
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-DB-NCBIHelper
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-FeatureIO
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-GFF3
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Glite
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Graphics
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-MAGETAB
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-NEXUS
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Phylo
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-SCF
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-Bio-Variation
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-BioPerl
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-BioPerl-Run
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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p5-transdecoder
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p5-TrimGalore
|
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paml
|
biology/paml: Update to 4.10.5
|
2022-08-26 01:22:46 -03:00 |
|
pbbam
|
*/*: bump all consumers after recent boost upgrade
|
2022-08-12 17:46:53 +03:00 |
|
pbseqan
|
*: fix tab vs. space issues, and comments according to the guide.
|
2021-10-16 11:51:39 +02:00 |
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peak-classifier
|
biology/peak-classifier: Update to 0.1.4
|
2022-06-11 09:26:57 -05:00 |
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pear-merger
|
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phrap
|
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phred
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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phyml
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
picard-tools
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
plink
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
pooler
|
biology/pooler: Update to 1.85
|
2022-07-12 07:47:45 -05:00 |
|
primer3
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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prodigal
|
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prodigy-lig
|
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protomol
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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psi88
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
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py-bcbio-gff
|
biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)
|
2022-02-03 13:38:42 -06:00 |
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py-biom-format
|
|
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|
py-biopython
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
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py-bx-python
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
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py-crossmap
|
biology/py-crossmap: Fix build with setuptools 58.0.0+
|
2022-03-25 21:38:04 +08:00 |
|
py-cutadapt
|
biology/py-cutadapt: fix tests by adding missing test depend
|
2022-04-07 21:59:32 +03:00 |
|
py-deeptools
|
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
|
2021-10-14 06:51:12 -05:00 |
|
py-deeptoolsintervals
|
biology/py-deeptoolsintervals: Python interface for deepTools interval trees
|
2021-10-13 11:02:13 -05:00 |
|
py-dna-features-viewer
|
biology/py-dna-features-viewer: Update to 3.1.1
|
2022-05-08 07:48:38 -05:00 |
|
py-dnaio
|
|
|
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py-ete3
|
biology/py-ete3: Add tests
|
2022-08-06 15:23:11 -07:00 |
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py-Genesis-PyAPI
|
|
|
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py-gffutils
|
biology/py-gffutils: Update 0.10.1 -> 0.11.0
|
2022-06-06 17:38:48 -07:00 |
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py-goatools
|
|
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py-gtfparse
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|
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py-hits
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|
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py-libnuml
|
biology/{,py-}libnuml: Update 1.1.5 -> 1.1.6
|
2022-04-23 18:36:56 -07:00 |
|
py-libsedml
|
biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32
|
2022-06-08 22:53:28 -07:00 |
|
py-loompy
|
biology/py-loompy: Update 3.0.6 -> 3.0.7
|
2022-03-06 09:09:59 -08:00 |
|
py-macs2
|
|
|
|
py-mrcfile
|
biology/py-mrcfile: Update 1.4.0 -> 1.4.2
|
2022-07-29 01:46:46 -07:00 |
|
py-multiqc
|
|
|
|
py-ont-fast5-api
|
biology/py-ont-fast5-api: Update to 4.0.2
|
2022-03-25 11:37:29 -05:00 |
|
py-orange3-bioinformatics
|
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
|
2022-01-23 21:56:25 +01:00 |
|
py-orange3-single-cell
|
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
|
2022-01-23 21:56:25 +01:00 |
|
py-pandas-charm
|
|
|
|
py-py2bit
|
biology/py-py2bit: Python interface for 2bit packed nucleotide files
|
2021-10-13 07:53:53 -05:00 |
|
py-pybigwig
|
biology/py-bigwig: Rename to biology/py-pybigwig
|
2021-10-13 16:21:32 -05:00 |
|
py-pyfaidx
|
|
|
|
py-pysam
|
biology/py-pysam: Remove BROKEN lines
|
2022-07-19 08:51:56 -07:00 |
|
py-PySCeS
|
biology/py-PySCeS: Update 1.0.1 -> 1.0.2
|
2022-05-20 15:02:59 -07:00 |
|
py-python-libsbml
|
biology/py-python-libsbml: limit supported python versions, fix build
|
2021-11-03 21:26:41 +03:00 |
|
py-pywgsim
|
biology/py-pywgsim: Modified wgsim genomic data simulator
|
2021-09-06 07:55:49 -05:00 |
|
py-resdk
|
biology/py-resdk: Update 14.1.0 -> 15.0.0
|
2022-06-06 17:38:49 -07:00 |
|
py-scikit-bio
|
biology/py-scikit-bio: Broken on aarch64
|
2022-06-03 15:56:03 -07:00 |
|
py-xenaPython
|
|
|
|
pyfasta
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
python-nexus
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
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rainbow
|
|
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|
rampler
|
|
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readseq
|
|
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recombine
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
ruby-bio
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
rubygem-bio
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
rubygem-bio-executables
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
rubygem-bio-old-biofetch-emulator
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
rubygem-bio-shell
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
sam2pairwise
|
biology/sam2pairwise: Show pairwise alignment for each read in a SAM file
|
2021-09-07 15:32:29 -05:00 |
|
samtools
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
scrm
|
|
|
|
seaview
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
seqan
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
seqan-apps
|
*/*: bump all consumers after recent boost upgrade
|
2022-08-12 17:46:53 +03:00 |
|
seqan1
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
seqan3
|
*/*: bump all consumers after recent boost upgrade
|
2022-08-12 17:46:53 +03:00 |
|
seqio
|
biology: remove 'Created by' lines
|
2022-07-20 16:20:57 +02:00 |
|
seqkit
|
all: Bump PORTREVISION after Go update
|
2022-08-03 16:35:13 -05:00 |
|
seqtk
|
biology/seqtk: Update to 1.3
|
2021-12-18 13:37:06 -06:00 |
|
sigviewer
|
|
|
|
sim4
|
biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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slclust
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smithwaterman
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snpeff
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cleanup: remove expired versions of OpenJDK (12 through 16)
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2022-05-24 22:09:35 +02:00 |
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spoa
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*/*: bump all consumers after recent boost upgrade
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2022-08-12 17:46:53 +03:00 |
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sra-tools
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science/hdf5: bump PORTREVISION of consumers
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2022-07-20 16:35:24 +02:00 |
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stacks
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star
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biology/star: Broken on systems where OpenMP isn't enabled
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2022-07-23 18:24:10 -07:00 |
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stringtie
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subread
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tabixpp
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taxonkit
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all: Bump PORTREVISION after Go update
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2022-08-03 16:35:13 -05:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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tRNAscan-SE
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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ucsc-userapps
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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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ugene
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biology/ugene: Correct BROKEN message
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2022-08-04 09:35:24 -07:00 |
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unikmer
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all: Bump PORTREVISION after Go update
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2022-08-03 16:35:13 -05:00 |
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vcf-split
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biology/vcf-split: Update to 0.1.5
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2022-06-11 09:26:56 -05:00 |
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vcf2hap
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biology/vcf2hap: Update to 0.1.6
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2022-06-11 09:26:57 -05:00 |
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vcflib
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Fix CONFLICTS_INSTALL in benchmarks and biology
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2022-06-29 16:53:54 +02:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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viennarna
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biology/viennarna: Update 2.5.0 -> 2.5.1
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2022-07-31 01:12:49 -07:00 |
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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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biology: remove 'Created by' lines
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2022-07-20 16:20:57 +02:00 |
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Makefile
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biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching
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2022-08-07 13:30:47 -07:00 |
