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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 0.1.3.31
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2021-08-27 20:28:10 -05:00 |
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artemis
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avida
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babel
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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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bamutil
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biology/bamutil: Update to 1.0.15
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2021-10-20 14:43:38 -05:00 |
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bbmap
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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 1.13
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2021-07-12 08:30:10 -05:00 |
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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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bioawk
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biococoa
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biolibc
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biology/biolibc: Update to 0.2.0.11
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2021-09-17 11:33:57 -05:00 |
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biolibc-tools
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biology/biolibc-tools: High-performance tools based on biolibc
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2021-08-30 08:09:23 -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: 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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biostar-tools
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biology/biostar-tools: Add py-deeptools to metaport deps
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2021-10-14 06:53:52 -05:00 |
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bolt-lmm
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bowtie
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bowtie2
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bwa
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canu
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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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checkm
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clustal-omega
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clustalw
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cufflinks
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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 2.0.12
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2021-10-12 12:40:55 -03:00 |
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dsr-pdb
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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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biology/emboss: Add "emboss" command in ${LOCALBASE}/bin
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2021-09-24 16:34:20 -05:00 |
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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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fasta3
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fastahack
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fastdnaml
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fastool
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fastp
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biology/fastp: Update to 0.23.1
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2021-10-20 11:37:39 -05:00 |
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fastqc
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fasttree
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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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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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garlic
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gatk
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gcta
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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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gff2ps
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gmap
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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gperiodic
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graphlan
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groopm
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haplohseq
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hhsuite
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biology/hhsuite: Fix build on aarch64
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2021-09-13 17:47:57 +02:00 |
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hisat2
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hmmer
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htslib
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biology/htslib: Add CPE information
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2021-09-10 21:18:20 +00:00 |
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hyphy
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biology/hyphy: Enable on aarch64.
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2021-10-08 18:27:33 +02:00 |
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igv
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cleanup: drop support for EOL FreeBSD 11.X
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2021-09-30 23:23:30 +02:00 |
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infernal
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iolib
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iqtree
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jalview
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cleanup: drop support for EOL FreeBSD 11.X
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2021-09-30 23:23:30 +02:00 |
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jellyfish
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*: Clean up some things
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2021-10-12 17:01:38 +02:00 |
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kallisto
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lamarc
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libbigwig
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libgtextutils
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libneurosim
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biology/libneurosim: New port: Common interfaces for neuronal simulators
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2021-10-08 10:20:27 -07:00 |
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libnuml
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biology/libnuml: New port: C++ library for Numerical Markup Language
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2021-09-18 23:47:02 -07:00 |
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libsbml
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libsedml
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biology/libsedml: New port: C++ SED-ML library
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2021-09-19 11:15:35 -07:00 |
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linux-foldingathome
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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mafft
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biology/mafft: Update to 7.267
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2021-10-22 13:11:23 +08:00 |
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mapm3
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migrate
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minimap2
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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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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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graphics/mesa-libs: Bump reverse deps for libglvnd
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2021-06-22 11:53:08 -07:00 |
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mopac
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mothur
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biology/mothur: Update 1.46.0 -> 1.46.1
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2021-09-02 02:29:56 -07:00 |
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mrbayes
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mummer
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muscle
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ncbi-blast+
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devel/grpc: Update to 1.41.0
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2021-10-25 23:57:13 +08:00 |
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ncbi-cxx-toolkit
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biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0
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2021-10-01 00:14:37 -07:00 |
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ncbi-entrez-direct
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ncbi-toolkit
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ncbi-vdb
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ngs-sdk
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biology/ngs-sdk: Update 2.11.0-> 2.11.1
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2021-08-18 10:17:44 -07:00 |
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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 0.1.1.21
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2021-09-02 18:15:40 -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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picard-tools
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plink
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pooler
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biology/pooler: fix build on powerpc
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2021-10-06 20:52:30 +00:00 |
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primer3
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prodigal
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prodigy-lig
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protomol
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psi88
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py-biom-format
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py-biopython
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biology/py-biopython: Update to 1.79
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2021-10-12 14:43:04 +08:00 |
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py-bx-python
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biology/py-bx-python: Update 0.8.10 -> 0.8.11-6
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2021-08-17 12:10:45 -07:00 |
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py-crossmap
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biology/py-crossmap: chase ad5a0604c4
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2021-10-14 00:53:16 +00:00 |
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py-cutadapt
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py-deeptools
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biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
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2021-10-14 06:51:12 -05:00 |
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py-deeptoolsintervals
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biology/py-deeptoolsintervals: Python interface for deepTools interval trees
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2021-10-13 11:02:13 -05:00 |
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py-dnaio
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py-ete3
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py-Genesis-PyAPI
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py-gffutils
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py-goatools
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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: Fix typo
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2021-09-19 11:15:35 -07:00 |
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py-libsedml
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biology/py-libsedml: New port: SED-ML library for Python
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2021-09-19 11:15:36 -07:00 |
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py-loompy
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py-macs2
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py-multiqc
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py-ont-fast5-api
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biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
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2021-08-13 08:34:09 -05:00 |
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py-orange3-bioinformatics
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py-orange3-single-cell
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py-pandas-charm
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py-py2bit
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biology/py-py2bit: Python interface for 2bit packed nucleotide files
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2021-10-13 07:53:53 -05:00 |
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py-pybigwig
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biology/py-bigwig: Rename to biology/py-pybigwig
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2021-10-13 16:21:32 -05:00 |
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py-pyfaidx
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py-pysam
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py-PySCeS
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biology/py-PySCeS: Update 0.9.8a -> 1.0.0
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2021-09-20 14:34:22 -07:00 |
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py-python-libsbml
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biology/py-python-libsbml: New port: LibSBML Python API
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2021-08-17 14:30:07 -07:00 |
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py-pywgsim
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biology/py-pywgsim: Modified wgsim genomic data simulator
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2021-09-06 07:55:49 -05:00 |
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py-resdk
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biology/py-resdk: Update 13.4.0 -> 13.6.0
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2021-10-22 01:57:04 -07:00 |
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py-scikit-bio
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py-xenaPython
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pyfasta
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python-nexus
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rainbow
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rampler
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readseq
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recombine
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ruby-bio
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rubygem-bio
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biology/rubygem-bio: Update to 2.0.2
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2021-07-01 04:44:06 +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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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 1.13
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2021-07-12 08:24:26 -05:00 |
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scrm
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seaview
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biology/seaview: in preparation to FLTK update, unbreak the port
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2021-08-14 08:58:03 +00:00 |
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seqan
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seqan1
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seqan3
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biology/seqan3: Add the 'test' target (currently broken due to lacking clang support)
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2021-08-13 10:08:56 -07:00 |
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seqan-apps
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*/*: Remove compiler:openmp from Mk/Uses/compiler.mk
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2021-10-03 19:47:27 +02:00 |
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seqio
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seqkit
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biology/seqkit: Update 0.16.1 -> 2.0.1
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2021-09-18 10:48:26 -07:00 |
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seqtk
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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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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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star
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stringtie
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subread
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tabixpp
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taxonkit
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treekin
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biology/treekin: Unbreak
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2021-10-15 08:50:24 -07:00 |
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treepuzzle
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trimadap
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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trimmomatic
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tRNAscan-SE
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ucsc-userapps
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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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ugene
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biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
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2021-10-14 11:23:37 +00:00 |
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unikmer
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biology/unikmer: Update 0.18.4 -> 0.18.8
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2021-09-26 01:54:07 -07:00 |
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vcf2hap
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biology/vcf2hap: Update to 0.1.3.12
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2021-08-27 20:32:51 -05:00 |
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vcf-split
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biology/vcf-split: Update to 0.1.2.14
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2021-08-27 20:30:52 -05:00 |
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vcflib
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vcftools
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biology/vcftools: Add CPE information
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2021-09-25 20:28:38 +00:00 |
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velvet
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viennarna
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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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Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
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2021-10-25 12:58:29 +00:00 |
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vt
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wise
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Makefile
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*/Makefile: Sort SUBDIRs
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2021-10-25 23:57:04 +08:00 |
