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abyss
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New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler
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2019-02-25 07:56:45 +00:00 |
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artemis
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biology/artemis: Update 9 -> 17.0.1-11
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2018-06-11 17:45:56 +00:00 |
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avida
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Change cmake default behaviour to outsource.
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2018-12-25 20:25:39 +00:00 |
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babel
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bamtools
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Change cmake default behaviour to outsource.
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2018-12-25 20:25:39 +00:00 |
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bcftools
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biology/bcftools: update to 1.9
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2018-08-02 19:30:57 +00:00 |
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bedtools
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biology/bedtools: unbreak with libc++ 8
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2019-03-04 06:55:08 +00:00 |
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biococoa
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Move Objective-C ports to the v2 GNUstep ABI.
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2019-02-03 15:37:58 +00:00 |
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bowtie
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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bowtie2
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Update devel/tbb to version 2019.1 and bump dependent ports' revisions
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2018-10-11 14:47:13 +00:00 |
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bwa
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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canu
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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cd-hit
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biology/cd-hit: Upgrade to 4.8.1
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2019-03-14 23:59:47 +00:00 |
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cdbfasta
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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checkm
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biology/checkm: Update 1.0.12 -> 1.0.13
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2019-02-09 22:58:09 +00:00 |
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chemeq
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clustal-omega
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biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw
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2018-05-21 22:15:26 +00:00 |
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clustalw
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biology/clustalw: Fix license, take maintainership
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2018-05-21 01:13:40 +00:00 |
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clustalx
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Mark QT4 ports/functionality for removal on 2019-03-15
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2018-12-02 15:41:47 +00:00 |
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consed
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cytoscape
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biology/cytoscape: Fix license
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2018-08-12 06:29:51 +00:00 |
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ddocent
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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diamond
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biology/diamond: Update to version 0.9.24
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2018-12-31 19:00:00 +00:00 |
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dsr-pdb
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biology/dsr-pdb: Correct typo
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2019-02-05 19:01:59 +00:00 |
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emboss
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exonerate
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New port: biology/exonerate: Generic tool for sequence alignment
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2018-07-13 07:02:16 +00:00 |
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fasta
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fasta3
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fastahack
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biology/fastahack: Utility for indexing and sequence extraction from FASTA files
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2018-04-16 14:50:46 +00:00 |
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fastdnaml
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fastool
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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fastqc
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fasttree
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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fastx-toolkit
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biology/fastx-toolkit: Fix build on FreeBSD 12
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2018-05-16 15:13:43 +00:00 |
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figtree
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New port: biology/figtree: Graphical viewer of phylogenetic trees
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2019-02-03 21:14:38 +00:00 |
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fluctuate
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freebayes
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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garlic
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Return maho@'s ports to the pool after his commit bit expired.
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2018-03-11 11:20:43 +00:00 |
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gatk
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devel/gradle: Update to 5.0
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2018-12-04 17:53:46 +00:00 |
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gff2ps
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biology/gff2ps: update 0.98d to 0.98l
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2018-12-19 17:34:29 +00:00 |
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gmap
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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gperiodic
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graphlan
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New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees
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2019-02-03 20:13:26 +00:00 |
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grappa
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groopm
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biology/groopm fails to build with python3
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2019-01-07 09:44:42 +00:00 |
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hisat2
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New port: biology/hisat2: Program for mapping next-generation sequencing reads
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2019-01-11 16:02:05 +00:00 |
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hmmer
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vec_splats function is not supported by base GCC. Add USES=compiler:c11
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2019-02-18 01:30:24 +00:00 |
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htslib
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biology/htslib: update to 1.9
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2018-08-02 19:27:13 +00:00 |
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hyphy
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Change cmake default behaviour to outsource.
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2018-12-25 20:25:39 +00:00 |
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igv
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biology/igv: Update 2.4.16 -> 2.4.19
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2019-02-23 21:23:51 +00:00 |
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infernal
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Allow building on powerpc64.
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2018-09-27 23:02:56 +00:00 |
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iolib
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Remove the incorrect typedefs to fix build on tier-2.
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2018-11-05 19:45:23 +00:00 |
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iqtree
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biology/iqtree: Update to version 1.6.10
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2019-02-21 14:33:43 +00:00 |
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jalview
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jellyfish
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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kallisto
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kallisto: Upgrade to 0.45.1, unbundle hstlib
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2019-02-24 20:32:19 +00:00 |
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lagan
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lamarc
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biology/lamarc: Fix build with Clang 6
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2018-08-25 03:13:37 +00:00 |
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libgtextutils
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biology/libgtextutils: Unbreak for FreeBSD 12
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2018-03-29 15:41:07 +00:00 |
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libsbml
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Change cmake default behaviour to outsource.
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2018-12-25 20:25:39 +00:00 |
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linux-foldingathome
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biology/linux-foldingathome: reset maintainer by request
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2018-07-27 02:19:43 +00:00 |
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mafft
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mapm3
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migrate
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Mark broken on armvX and mips.
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2018-03-18 13:48:07 +00:00 |
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molden
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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mopac
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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mrbayes
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mummer
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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muscle
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ncbi-blast+
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Update dns/libidn2 to 2.1.1
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2019-02-09 23:25:36 +00:00 |
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ncbi-cxx-toolkit
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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ncbi-toolkit
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Update dns/libidn2 to 2.1.1
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2019-02-09 23:25:36 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Update 2.9.3 -> 2.9.4
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2019-02-23 21:55:55 +00:00 |
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p5-AcePerl
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-ASN1-EntrezGene
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Update to 1.73
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2018-10-10 10:23:10 +00:00 |
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p5-Bio-Cluster
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Add p5-Bio-Cluster 1.7.3
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2019-02-20 20:46:37 +00:00 |
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p5-Bio-Coordinate
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-Das
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-Das-Lite
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-FeatureIO
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-GFF3
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-Glite
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-Graphics
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-MAGETAB
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-NEXUS
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-Phylo
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-SCF
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-BioPerl
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Update to 1.007005 (1.7.5)
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2019-02-22 19:54:12 +00:00 |
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p5-BioPerl-Run
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Update to 1.007003
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2019-02-20 20:46:58 +00:00 |
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p5-transdecoder
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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p5-TrimGalore
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paml
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biology/paml: Update to version 4.9i
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2019-02-26 15:12:42 +00:00 |
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pbbam
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biology/pbbam: Upgrade to 0.18.0 release
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2019-02-19 23:03:41 +00:00 |
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pbcopper
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biology/pbcopper: Upgrade to 0.4.1 release
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2019-02-19 22:20:11 +00:00 |
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pbseqan
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biology/pbseqan: Mark deprecated
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2019-02-20 01:53:35 +00:00 |
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pear-merger
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Mark as broken on aarch64, and, where appropriate, armvX.
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2018-06-21 23:52:37 +00:00 |
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phrap
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Add DOCS options to ports that should have one.
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2018-09-10 13:14:50 +00:00 |
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phred
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Add DOCS options to ports that should have one.
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2018-09-10 13:14:50 +00:00 |
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phylip
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phyml
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Change 4 ports from net/mpich2 to net/mpich
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2018-09-22 18:00:24 +00:00 |
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plinkseq
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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primer3
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biology/primer3: Fix build with Clang 6
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2018-08-25 03:35:46 +00:00 |
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prodigal
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New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes
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2019-02-03 18:08:14 +00:00 |
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prodigy-lig
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New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities
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2019-02-03 18:49:23 +00:00 |
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protomol
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biology/protomol: Fix doubled USES overwriting the old value
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2018-08-25 03:47:25 +00:00 |
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psi88
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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py-biom-format
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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py-biopython
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- Update to 1.73
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2018-12-22 04:54:51 +00:00 |
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py-bx-python
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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py-cutadapt
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biology/py-cutadapt: Upgrade to 1.18
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2018-09-20 14:10:52 +00:00 |
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py-fastTSNE
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New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE
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2018-12-15 08:58:05 +00:00 |
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py-Genesis-PyAPI
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Use PY_FLAVOR for dependencies.
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2018-06-20 17:05:41 +00:00 |
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py-gffutils
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New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework
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2018-10-19 02:06:53 +00:00 |
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py-gtfparse
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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py-loompy
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biology/py-loompy: Update 2.0.16 -> 2.0.17
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2019-02-02 21:38:48 +00:00 |
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py-macs2
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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py-orange3-bioinformatics
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Fix Qt5 symbol version scripts to put the catch-all clause first. When
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2019-01-16 11:13:44 +00:00 |
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py-orange3-single-cell
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Fix Qt5 symbol version scripts to put the catch-all clause first. When
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2019-01-16 11:13:44 +00:00 |
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py-pyfaidx
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biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2
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2018-10-28 04:34:14 +00:00 |
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py-pysam
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biology/py-pysam: Update 0.15.1 -> 0.15.2
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2019-01-26 04:15:54 +00:00 |
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pycogent
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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pyfasta
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- Update WWW
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2019-02-07 09:30:40 +00:00 |
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python-nexus
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- Update to 1.63
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2018-09-22 08:54:58 +00:00 |
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rainbow
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biology/rainbow: Efficient clustering and assembling of short reads
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2018-04-02 16:50:46 +00:00 |
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recombine
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ruby-bio
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rubygem-bio
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Update to 1.5.2
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2018-09-21 18:08:24 +00:00 |
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samtools
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biology/samtools: update to 1.9
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2018-08-02 19:28:36 +00:00 |
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seaview
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biology/seaview: Fix build with Clang 6
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2018-09-08 09:01:35 +00:00 |
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seqan
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biology/seqan-apps, biology/seqan: Update to 2.4.0
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2018-03-10 06:21:37 +00:00 |
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seqan1
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seqan-apps
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Change cmake default behaviour to outsource.
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2018-12-25 20:25:39 +00:00 |
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seqio
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seqtk
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biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
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2018-04-03 20:57:05 +00:00 |
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seqtools
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biology/seqtools: fix build on current, if lld is lld7
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2019-01-07 19:54:40 +00:00 |
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sim4
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slclust
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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smithwaterman
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biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
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2018-04-15 17:45:52 +00:00 |
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stacks
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biology/stacks: Upgrade to 2.3
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2019-01-12 15:53:00 +00:00 |
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stringtie
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New port: biology/stringtie: Transcript assembly and quantification for RNA-seq
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2018-07-11 21:32:39 +00:00 |
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t_coffee
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-12-12 01:35:33 +00:00 |
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tabixpp
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biology/tabixpp: C++ wrapper to tabix indexer
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2018-04-14 23:52:16 +00:00 |
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treepuzzle
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trimadap
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Mark as broken on aarch64, and, where appropriate, armvX.
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2018-06-21 23:52:37 +00:00 |
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trimmomatic
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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tRNAscan-SE
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- Unbreak by adding missing pkg-plist
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2018-09-28 00:12:48 +00:00 |
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ugene
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Fix Qt5 symbol version scripts to put the catch-all clause first. When
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2019-01-16 11:13:44 +00:00 |
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unanimity
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biology/unanimity: Upgrade to 3.4.1
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2019-02-24 16:04:58 +00:00 |
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vcflib
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Mark these ports as broken on aarch64.
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2018-06-22 00:03:08 +00:00 |
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vcftools
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biology/vcftools: Update to 0.1.16, a security release
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2018-08-04 01:29:29 +00:00 |
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velvet
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- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
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2018-01-11 18:09:00 +00:00 |
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wise
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Makefile
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New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end sequence assembler
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2019-02-25 07:56:45 +00:00 |
