| .. |
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abyss
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biology/abyss: Update 2.3.0-3 -> 2.3.1
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2021-04-22 10:18:02 -07:00 |
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ad2vcf
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biology/ad2vcf: Remove comment used to silence portlint
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2021-06-11 10:39:02 -05:00 |
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artemis
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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avida
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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babel
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all: Remove all other $FreeBSD keywords.
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2021-04-06 16:31:13 +02:00 |
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bamtools
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biology/bamtools: Update to 2.5.2
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2021-07-06 13:10:54 -05:00 |
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bbmap
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biology/bbmap: BBMap short read aligner, and other bioinformatic tools
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2021-04-18 11:21:29 -05:00 |
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bcftools
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biology/bcftools: Update to 1.13
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2021-07-12 08:30:10 -05:00 |
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bedtools
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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bioawk
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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biococoa
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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biolibc
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biology/biolibc: Remove comment used to silence portlint
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2021-06-11 10:38:27 -05:00 |
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bioparser
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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biosig
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biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX
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2021-08-16 19:57:30 -07:00 |
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biosoup
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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biostar-tools
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biostar-tools: Correct category for py-ont-fast5-api
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2021-08-13 09:16:27 -05:00 |
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bolt-lmm
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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bowtie
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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bowtie2
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biology/bowtie2: Update to 2.4.4
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2021-05-24 11:35:43 -05:00 |
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bwa
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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canu
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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cd-hit
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biology/cd-hit: fix build on powerpc
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2021-06-10 00:35:36 +00:00 |
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cdbfasta
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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checkm
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math/py-matplotlib: chase minimum Python version in dependent ports
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2021-05-10 22:13:20 +02:00 |
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clustal-omega
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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clustalw
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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cufflinks
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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cytoscape
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biology/cytoscape: mark unconditionally BROKEN
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2021-05-12 14:55:52 +03:00 |
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ddocent
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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diamond
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biology/diamond: Update to 2.0.11-1
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2021-07-06 10:15:24 -03:00 |
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dsr-pdb
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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edlib
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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emboss
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +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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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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fasta
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Deorbit RESTRICTED && NO_CDROM, part two.
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2021-05-06 13:47:48 +02:00 |
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fasta3
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Deorbit RESTRICTED && NO_CDROM, part one.
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2021-05-06 13:47:41 +02:00 |
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fastahack
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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fastdnaml
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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fastool
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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fastp
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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fastqc
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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fasttree
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biology/fasttree: fix build on armv7
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2021-06-15 08:41:19 +00:00 |
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fastx-toolkit
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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figtree
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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fluctuate
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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freebayes
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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garlic
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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gatk
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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gcta
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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gemma
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math/gsl: update to 2.7
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2021-06-16 21:31:27 +02:00 |
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generand
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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gff2ps
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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gmap
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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gperiodic
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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graphlan
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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groopm
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math/py-matplotlib: chase minimum Python version in dependent ports
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2021-05-10 22:13:20 +02:00 |
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haplohseq
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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hhsuite
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biology/hhsuite: fix build on powerpc64*
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2021-07-08 13:13:54 +00:00 |
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hisat2
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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hmmer
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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htslib
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htslib: Update to 1.13
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2021-07-12 08:16:45 -05:00 |
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hyphy
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biology/hyphy: Update to 2.5.31
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2021-06-05 20:00:24 -03:00 |
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igv
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biology/igv: Fix build
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2021-06-27 05:33:51 -04:00 |
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infernal
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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iolib
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biology/iolib: Drop maintainership
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2021-05-19 20:56:24 +01:00 |
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iqtree
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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jalview
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biology/jalview: Fix build
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2021-06-27 05:30:39 -04:00 |
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jellyfish
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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kallisto
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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lamarc
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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libbigwig
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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libgtextutils
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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libsbml
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biology/libsbml: Rename LIBXML option to LIBXML2
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2021-05-12 05:46:56 +08:00 |
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linux-foldingathome
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biology/linux-foldingathome: Update to 7.6.21
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2021-06-25 19:13:19 +02:00 |
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mafft
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
|
mapm3
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
|
migrate
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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minimap2
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biology/minimap2: Update to 2.20
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2021-05-29 16:06:34 -05:00 |
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mmseqs2
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biology/mmseqs2: Fix runtime error when built with clang
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2021-06-29 09:04:48 -05:00 |
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molden
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graphics/mesa-libs: Bump reverse deps for libglvnd
|
2021-06-22 11:53:08 -07:00 |
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mopac
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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mothur
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biology/mothur: Update 1.45.2 -> 1.45.3
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2021-05-09 09:11:11 -07:00 |
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mrbayes
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*: Remove unnecessary 'port' argument from USES=readline
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2021-05-15 09:14:04 +02:00 |
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mummer
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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muscle
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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ncbi-blast+
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biology/ncbi-blast+: Update to 2.12.0
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2021-07-02 11:48:20 -05:00 |
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ncbi-cxx-toolkit
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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ncbi-entrez-direct
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biology/ncbi-entrez-direct: Update to 14.9.20210423_1
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2021-04-26 11:53:11 -05:00 |
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ncbi-toolkit
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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ncbi-vdb
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devel/libepoll-shim: update to 0.0.20210418
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2021-04-26 14:17:32 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH
|
2021-04-15 10:01:31 -07:00 |
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p5-AcePerl
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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p5-Bio-ASN1-EntrezGene
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Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Cluster
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Coordinate
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Das
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Das-Lite
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-DB-EMBL
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
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
|
Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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p5-Bio-GFF3
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Glite
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Graphics
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-MAGETAB
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-NEXUS
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Phylo
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-SCF
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-Bio-Variation
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-BioPerl
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-BioPerl-Run
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
p5-transdecoder
|
One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
|
p5-TrimGalore
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
paml
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
pbbam
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
pbseqan
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
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peak-classifier
|
biology/peak-classifier: Classify peaks based on GFF features
|
2021-06-14 11:40:33 -05:00 |
|
pear-merger
|
One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
|
phrap
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
phred
|
Deorbit RESTRICTED && NO_CDROM, part two.
|
2021-05-06 13:47:48 +02:00 |
|
phyml
|
Clean up some things
|
2021-04-15 10:31:56 +02:00 |
|
picard-tools
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
plink
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
pooler
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
primer3
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
prodigal
|
One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
|
prodigy-lig
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
protomol
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
psi88
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
py-bigwig
|
biology/py-bigwig: Fix packaging with Python 3.8+
|
2021-04-21 09:41:29 +02:00 |
|
py-biom-format
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-biopython
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
py-bx-python
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
py-crossmap
|
biology/py-crossmap: Update to 0.5.4
|
2021-04-21 08:31:13 -05:00 |
|
py-cutadapt
|
biology/py-cutadapt: Update strict py-dnaio dep version
|
2021-05-04 08:20:39 -05:00 |
|
py-dnaio
|
biology/py-dnaio: Update to 0.5.1
|
2021-05-04 08:19:25 -05:00 |
|
py-ete3
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-Genesis-PyAPI
|
One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
|
py-gffutils
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-goatools
|
biology/py-goatools: Tools for processing and visualizing Gene Ontology terms
|
2021-07-02 12:00:29 -05:00 |
|
py-gtfparse
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-hits
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One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-loompy
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-macs2
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-multiqc
|
math/py-matplotlib: chase minimum Python version in dependent ports
|
2021-05-10 22:13:20 +02:00 |
|
py-ont-fast5-api
|
biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
|
2021-08-13 08:34:09 -05:00 |
|
py-orange3-bioinformatics
|
biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1
|
2021-04-27 01:56:19 -07:00 |
|
py-orange3-single-cell
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-pandas-charm
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-pyfaidx
|
biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5
|
2021-04-23 14:57:50 -07:00 |
|
py-pysam
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-resdk
|
biology/py-resdk: Update 13.2.0 -> 13.3.0
|
2021-05-24 00:26:50 -07:00 |
|
py-scikit-bio
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
py-xenaPython
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
pyfasta
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
python-nexus
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
rainbow
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
rampler
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
readseq
|
biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint
|
2021-04-18 09:20:28 -05:00 |
|
recombine
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
ruby-bio
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
rubygem-bio
|
biology/rubygem-bio: Update to 2.0.2
|
2021-07-01 04:44:06 +08:00 |
|
rubygem-bio-executables
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
rubygem-bio-old-biofetch-emulator
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
rubygem-bio-shell
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
samtools
|
biology/samtools: Update to 1.13
|
2021-07-12 08:24:26 -05:00 |
|
scrm
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
seaview
|
biology/seaview: in preparation to FLTK update, unbreak the port
|
2021-08-14 08:58:03 +00:00 |
|
seqan
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
seqan1
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
seqan3
|
biology/seqan3: Add the 'test' target (currently broken due to lacking clang support)
|
2021-08-13 10:08:56 -07:00 |
|
seqan-apps
|
biology/seqan-apps: fix packaging on armv7
|
2021-06-21 08:11:25 +00:00 |
|
seqio
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
seqkit
|
biology/seqkit: Add 'test' target
|
2021-08-14 11:53:27 -07:00 |
|
seqtk
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
sigviewer
|
biology/sigviewer: New port: Viewing application for biosignals
|
2021-08-17 00:05:37 -07:00 |
|
sim4
|
Remove # $FreeBSD$ from Makefiles.
|
2021-04-06 16:31:07 +02:00 |
|
slclust
|
One more small cleanup, forgotten yesterday.
|
2021-04-07 10:09:01 +02:00 |
|
smithwaterman
|
One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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snpeff
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biology/snpeff: Improvements to Makefile and patches
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2021-04-19 11:41:58 -05:00 |
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spoa
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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sra-tools
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biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives
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2021-06-22 12:55:15 -05:00 |
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stacks
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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star
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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stringtie
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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subread
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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tabixpp
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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taxonkit
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biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit
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2021-05-26 15:25:22 -07:00 |
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treekin
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math/lapack: +math/blas et al., upgrade to 3.9.1
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2021-06-13 19:48:12 +02:00 |
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treepuzzle
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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trimadap
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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trimmomatic
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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tRNAscan-SE
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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ucsc-userapps
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biology/ucsc-userapps: Update to v414
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2021-05-15 10:23:08 -05:00 |
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ugene
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biology/ugene: update Unipro UGENE to version 39.0.
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2021-06-25 17:56:47 +00:00 |
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unikmer
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biology/unikmer: Add 'test' target
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2021-08-14 11:35:11 -07:00 |
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vcf2hap
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biology/vcf2hap: Remove comment used to silence portlint
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2021-06-11 10:40:11 -05:00 |
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vcf-split
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biology/vcf-split: Update to 0.1.2
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2021-06-11 10:05:19 -05:00 |
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vcflib
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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vcftools
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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velvet
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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viennarna
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math/gsl: update to 2.7
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2021-06-16 21:31:27 +02:00 |
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vsearch
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biology/vsearch: Update to 2.17.1
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2021-06-19 07:33:58 -05:00 |
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vt
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One more small cleanup, forgotten yesterday.
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2021-04-07 10:09:01 +02:00 |
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wise
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Remove # $FreeBSD$ from Makefiles.
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2021-04-06 16:31:07 +02:00 |
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Makefile
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biology/sigviewer: New port: Viewing application for biosignals
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2021-08-17 00:05:37 -07:00 |
