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abyss
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Chanse update of devel/libffi
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2020-07-04 18:11:42 +00:00 |
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artemis
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avida
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babel
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bamtools
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Bump devel/jsoncpp consumers after r540853.
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2020-06-30 17:46:18 +00:00 |
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bcftools
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biology/bcftools: Upgrade to 1.10.2
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2020-08-03 18:16:54 +00:00 |
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bedtools
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bioawk
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biology/bioawk: BWK awk modified for biological data
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2020-06-05 02:45:33 +00:00 |
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biococoa
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bolt-lmm
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Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
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2020-05-06 16:11:14 +00:00 |
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bowtie
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biology/bowtie: Unbreak build with GCC 10
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2020-07-04 10:46:08 +00:00 |
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bowtie2
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Update devel/tbb to 2020.3 and bump dependent ports' revisions
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2020-07-17 10:12:25 +00:00 |
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bwa
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canu
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Mark as BROKEN on powerpc64:
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2020-05-17 02:25:16 +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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cufflinks
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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cytoscape
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ddocent
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diamond
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biology/diamond: Update to version 2.0.2
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2020-08-07 11:20:11 +00:00 |
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dsr-pdb
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emboss
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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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gatk
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biology/gatk: Update 4.1.7.0 -> 4.1.8.0
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2020-07-09 00:40:56 +00:00 |
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gcta
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Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
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2020-05-06 16:11:14 +00:00 |
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gemma
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Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
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2020-05-06 16:39:12 +00:00 |
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gff2ps
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gmap
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gperiodic
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graphlan
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biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed
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2020-08-14 04:59:29 +00:00 |
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grappa
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groopm
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biology/groopm: Remove python's 2.7 restriction placed here by mistake
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2020-08-13 19:19:23 +00:00 |
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haplohseq
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hhsuite
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biology/hhsuite: fix build on powerpc64 elfv2
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2020-05-11 19:33:32 +00:00 |
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hisat2
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hmmer
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htslib
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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hyphy
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biology/hyphy: Update to version 2.5.15
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2020-06-28 16:40:33 +00:00 |
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igv
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infernal
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iolib
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iqtree
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biology/iqtree: Update to version 2.0.6
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2020-05-30 18:43:26 +00:00 |
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jalview
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jellyfish
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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kallisto
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biology/kallisto: Revert to 0.46.1
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2020-08-03 15:45:21 +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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Move devel/swig30 to devel/swig and update to 4.0.1
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2020-06-17 18:17:45 +00:00 |
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linux-foldingathome
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Update to 7.6.13
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2020-05-09 13:21:29 +00:00 |
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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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mopac
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mothur
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Update devel/gmake to 4.3.
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2020-05-09 19:24:49 +00:00 |
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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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Bump PORTREVISION for security/nettle shlib change
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2020-05-16 10:51:32 +00:00 |
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ncbi-cxx-toolkit
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ncbi-toolkit
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Bump PORTREVISION for security/nettle shlib change
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2020-05-16 10:51:32 +00:00 |
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ngs-sdk
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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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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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Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
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2020-06-26 11:55:23 +00:00 |
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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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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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pbcopper
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Deprecate ports broken for more than 6 months
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2020-07-26 07:32:00 +00:00 |
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pbseqan
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pear-merger
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phrap
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Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
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2020-05-27 11:59:13 +00:00 |
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phred
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phylip
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phyml
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biology/phyml: update to 3.3.20200621
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2020-07-10 09:45:48 +00:00 |
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picard-tools
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biology/picard-tools: CLI tools for manipulating sequencing data
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2020-06-13 13:54:47 +00:00 |
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plink
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Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
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2020-05-06 16:39:12 +00:00 |
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primer3
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prodigal
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prodigy-lig
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Unbreak bulk -a
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2020-06-13 15:05:44 +00:00 |
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protomol
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psi88
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biology/psi88: Unbreak build with GCC 10
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2020-07-04 12:15:58 +00:00 |
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py-biopython
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biology/py-biopython: Set python requirement to 3.6+
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2020-06-13 13:42:12 +00:00 |
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py-bx-python
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biology/py-bx-python: Update 0.8.8 -> 0.8.9
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2020-06-26 04:17:11 +00:00 |
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py-cutadapt
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py-dnaio
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biology/py-dnaio: Upgrade to 0.4.2
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2020-05-24 15:23:15 +00:00 |
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py-ete3
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New port: biology/py-ete3: Framework for the analysis and visualization of trees
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2020-05-16 00:13:09 +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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Unbreak bulk -a
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2020-07-14 07:59:28 +00:00 |
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py-gtfparse
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biology/py-gtfparse: Update 1.2.0 -> 1.2.1
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2020-08-07 04:13:00 +00:00 |
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py-hits
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New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
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2020-05-16 03:11:05 +00:00 |
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py-loompy
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biology/py-loompy: Update 2.0.17 -> 3.0.6
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2020-06-16 02:26:08 +00:00 |
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py-macs2
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py-multiqc
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py-orange3-bioinformatics
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py-orange3-single-cell
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Update Sphinx
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2020-05-11 23:51:58 +00:00 |
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py-pandas-charm
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Clean up some things
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2020-05-30 00:57:02 +00:00 |
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py-pyfaidx
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py-pysam
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biology/py-pysam: Update 0.15.4 -> 0.16.0
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2020-06-09 05:03:48 +00:00 |
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py-scikit-bio
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devel/ipython: Update to 7.17.0
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2020-08-15 12:50:57 +00:00 |
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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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recombine
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ruby-bio
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rubygem-bio
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Update to 2.0.1
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2020-07-24 07:49:43 +00:00 |
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rubygem-bio-executables
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Add rubygem-bio-executables 1.0.0
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2020-07-24 07:08:00 +00:00 |
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rubygem-bio-old-biofetch-emulator
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Add rubygem-bio-old-biofetch-emulator 1.0.0
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2020-07-24 07:08:05 +00:00 |
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rubygem-bio-shell
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Add rubygem-bio-shell 1.0.0
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2020-07-24 07:08:11 +00:00 |
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samtools
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biology/samtools: Upgrade to 1.10
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2020-08-03 18:22:06 +00:00 |
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scrm
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Add compiler:c++11-lang to USES to fix build on GCC-based systems:
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2020-05-15 07:30:34 +00:00 |
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seaview
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biology/seaview: Update version 5.0.3=>5.0.4
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2020-06-22 17:34:44 +00:00 |
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seqan
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seqan1
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seqan-apps
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seqio
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seqtk
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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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stringtie
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subread
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biology/subread: Read alignment, quantification and mutation discovery
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2020-06-05 01:55:49 +00:00 |
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tabixpp
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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tophat
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treekin
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treepuzzle
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trimadap
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trimmomatic
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tRNAscan-SE
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ugene
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biology/ugene: prepare for Qt5-5.15
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2020-05-19 18:00:02 +00:00 |
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vcflib
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biology/htslib: Upgrade to 1.10.2
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2020-08-03 17:40:04 +00:00 |
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vcftools
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velvet
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viennarna
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vsearch
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biology/vsearch: Update to 2.15.0
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2020-06-20 14:31:59 +00:00 |
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vt
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biology/vt: Patch to work with htslib 1.10.2
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2020-08-03 17:42:32 +00:00 |
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wise
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Makefile
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Remove deprecated ports:
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2020-08-15 10:50:58 +00:00 |
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