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abyss
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biology/abyss: Update 2.1.5 -> 2.2.3
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2020-01-13 04:06:14 +00:00 |
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artemis
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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avida
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biology/avida: unbreak on powerpc64
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2019-10-23 16:25:10 +00:00 |
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babel
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bamtools
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bcftools
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math/gsl: update to 2.6
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2019-10-25 23:41:34 +00:00 |
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bedtools
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biology/bedtools: Upgrade to 2.29.2
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2019-12-19 01:04:11 +00:00 |
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biococoa
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bolt-lmm
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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bowtie
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bowtie2
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Update devel/tbb to 2020.0 and bump dependent ports' revisions [1]
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2019-12-26 16:25:22 +00:00 |
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bwa
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canu
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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cd-hit
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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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consed
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Mark a few ports BROKEN, unfetchable
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2019-11-06 12:48:32 +00:00 |
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cufflinks
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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cytoscape
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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ddocent
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diamond
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biology/diamond: Update to v0.9.29
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2019-11-20 17:14:29 +00:00 |
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dsr-pdb
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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emboss
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Sprinkle more USES=xorg
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2019-11-07 20:19:59 +00:00 |
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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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fastqc
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fasttree
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fastx-toolkit
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figtree
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fluctuate
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freebayes
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garlic
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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gatk
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biology/gatk: Update 4.1.2.0-43 -> 4.1.3.0
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2020-01-05 10:33:08 +00:00 |
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gemma
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math/gsl: update to 2.6
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2019-10-25 23:41:34 +00:00 |
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gff2ps
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gmap
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gperiodic
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a-b: Add missing USES={gnome,php,sdl,xorg}
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2019-11-08 09:27:56 +00:00 |
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graphlan
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grappa
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groopm
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haplohseq
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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hhsuite
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hisat2
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hmmer
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htslib
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hyphy
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igv
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infernal
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iolib
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iqtree
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jalview
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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jellyfish
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kallisto
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biology/kallisto: Upgrade to 0.46.1
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2019-11-06 00:18:14 +00:00 |
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lagan
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lamarc
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libbigwig
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libgtextutils
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libsbml
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mafft
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mapm3
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migrate
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minimap2
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molden
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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mopac
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mothur
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mrbayes
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Mark a few ports BROKEN, unfetchable
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2019-11-06 12:48:32 +00:00 |
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mummer
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muscle
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ncbi-blast+
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biology/ncbi-blast+: Upgrade to 2.10.0
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2019-12-26 16:21:17 +00:00 |
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ncbi-cxx-toolkit
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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ncbi-toolkit
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ngs-sdk
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biology/ngs-sdk: Update 2.10.0 -> 2.10.1
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2020-01-12 02:43:06 +00:00 |
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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Update *_DEPENDS
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2020-01-08 18:36:30 +00:00 |
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p5-Bio-Cluster
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Update *_DEPENDS
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2019-12-08 16:57:18 +00:00 |
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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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Add p5-Bio-DB-EMBL 1.7.4
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2019-12-08 16:49:19 +00:00 |
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p5-Bio-DB-NCBIHelper
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Add p5-Bio-DB-NCBIHelper 1.7.6
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2019-12-08 16:49:25 +00:00 |
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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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Update to 1.7.5
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2020-01-08 18:36:35 +00:00 |
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p5-BioPerl
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Update to 1.007007 (1.7.7)
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2019-12-08 16:57:23 +00:00 |
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p5-BioPerl-Run
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Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago
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2020-01-08 18:36:40 +00:00 |
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p5-transdecoder
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p5-TrimGalore
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biology/p5-TrimGalore: Upgrade to 0.6.5
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2019-11-26 16:20:12 +00:00 |
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paml
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biology/paml: Update to version 4.9j
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2019-11-22 15:32:40 +00:00 |
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pbbam
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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pbcopper
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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pbseqan
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biology/unanimity and dependencies: Flag as no longer open source
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2019-11-24 15:53:00 +00:00 |
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pear-merger
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phrap
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phred
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phylip
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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phyml
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biology/phyml: disable -march=native
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2019-12-06 13:04:41 +00:00 |
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plinkseq
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Mark a few ports BROKEN, unfetchable
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2019-11-06 12:48:32 +00:00 |
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primer3
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prodigal
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biology/prodigal: Eliminate a very old version from the portscout discovery process
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2019-10-12 15:40:21 +00:00 |
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prodigy-lig
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protomol
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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psi88
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py-biom-format
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- Limit python version (does not build with 3.7+)
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2019-11-08 12:12:42 +00:00 |
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py-biopython
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py-bx-python
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biology/py-bx-python: Update 0.8.4 -> 0.8.6
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2019-11-23 05:53:50 +00:00 |
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py-cutadapt
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biology/py-cutadapt: Upgrade to 2.7
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2019-11-23 14:45:53 +00:00 |
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py-dnaio
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biology/py-dnaio: Upgrade to 0.4.1
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2019-11-23 14:40:00 +00:00 |
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py-fastTSNE
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py-Genesis-PyAPI
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py-gffutils
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biology/py-gffutils: Update 0.9 -> 0.10
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2019-12-31 05:16:09 +00:00 |
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py-gtfparse
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py-loompy
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py-macs2
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biology/py-macs2: Upgrade to 2.2.6
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2020-01-11 14:20:00 +00:00 |
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py-multiqc
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biology/py-multiqc: Upgrade to 1.8
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2019-11-26 16:25:08 +00:00 |
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py-orange3-bioinformatics
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py-orange3-single-cell
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py-pyfaidx
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py-pysam
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py-xenaPython
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pycogent
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Deprecate a few ports
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2019-12-26 07:54:28 +00:00 |
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pyfasta
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python-nexus
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rainbow
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recombine
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ruby-bio
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rubygem-bio
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samtools
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seaview
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Add USES=xorg USES=gl, ports categories b
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2019-11-04 21:08:20 +00:00 |
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seqan
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seqan1
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seqan-apps
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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seqio
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seqtk
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seqtools
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Mark a few ports BROKEN, unfetchable
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2019-11-06 12:48:32 +00:00 |
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sim4
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slclust
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smithwaterman
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stacks
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star
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biology/star: Upgrade to 2.7.2d
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2019-10-06 22:18:31 +00:00 |
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stringtie
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t_coffee
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Mark a few ports BROKEN, unfetchable
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2019-11-06 12:48:32 +00:00 |
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tabixpp
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tophat
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devel/boost-*: update to 1.72.0
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2019-12-11 17:53:48 +00:00 |
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treekin
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treepuzzle
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trimadap
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trimmomatic
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Clean up after java/openjdk6 and java/openjdk6-jre removal
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2019-11-26 21:46:12 +00:00 |
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tRNAscan-SE
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ugene
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Mark a few ports BROKEN, unfetchable
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2019-11-06 12:48:32 +00:00 |
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unanimity
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Mark a few ports broken (unfetchable)
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2020-01-05 10:26:04 +00:00 |
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vcflib
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vcftools
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velvet
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viennarna
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biology/viennarna: Update 2.4.13 -> 2.4.14
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2020-01-06 04:17:48 +00:00 |
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vsearch
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wise
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a-b: Add missing USES={gnome,php,sdl,xorg}
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2019-11-08 09:27:56 +00:00 |
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Makefile
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Add p5-Bio-Variation 1.7.4
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2019-12-08 16:49:31 +00:00 |
