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abyss
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biology/abyss: fix build on big-endian architectures
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2019-06-21 11:43:09 +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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bolt-lmm
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biology/bolt-lmm: Mixed model association testing and variance component analysis
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2019-05-26 03:36:49 +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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biology/bowtie2: Clarify CPU-specificity
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2019-04-24 17:41:27 +00:00 |
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bwa
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canu
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biology/canu: Fix build on powerpc64 and aarch64
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2019-04-18 12:15:56 +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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checkm
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Bump a few PORTREVISIONs after r498529
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2019-04-10 06:18:31 +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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consed
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cufflinks
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biology/cufflinks: Fix build on i386 by removing the hard-coded -m64
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2019-05-29 07:02:28 +00:00 |
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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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biology/ddocent: Upgrade to 2.7.8
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2019-05-04 15:09:10 +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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devel/boost-*: update to 1.70.0
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2019-04-12 06:36:31 +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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fastp
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biology/fastp: Remove redundant USE_GCC
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2019-05-20 23:41:08 +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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gemma
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biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC
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2019-05-18 22:41:15 +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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Enable workaround for building on powerpc64.
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2019-06-21 11:15:08 +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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hhsuite
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biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist or isn't detected.
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2019-05-22 02:50:56 +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 2.5.2 -> 2.5.3
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2019-06-01 20:49:20 +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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- Fix build in head i386
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2019-04-01 19:33:15 +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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biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64
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2019-05-13 16:23:35 +00:00 |
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kallisto
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biology/kallisto: Upgrade to 0.46.0
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2019-06-12 15:24:55 +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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Use USES=pathfix
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2019-06-22 21:48:14 +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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minimap2
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biology/minimap2: Upgrade to 2.17
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2019-05-05 14:56:07 +00:00 |
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molden
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Related to revision 499061 bump ports with USES=fortran to have them
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2019-04-22 13:16:33 +00:00 |
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mopac
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Related to revision 499061 bump ports with USES=fortran to have them
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2019-04-22 13:16:33 +00:00 |
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mothur
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biology/mothur: Update 1.42.1-3 -> 1.42.2
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2019-06-19 23:54:44 +00:00 |
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mrbayes
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Update devel/readline to 8.0
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2019-04-09 14:04:49 +00:00 |
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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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biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl
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2019-06-14 00:37:59 +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 2.9.4 -> 2.9.6
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2019-03-31 03:31:59 +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 typo
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2019-04-23 14:11:50 +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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- Add LICENSE
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2019-03-30 09:01:08 +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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biology/p5-TrimGalore: Upgrade to 0.6.1
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2019-03-24 21:44:17 +00:00 |
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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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devel/boost-*: update to 1.70.0
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2019-04-12 06:36:31 +00:00 |
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pbcopper
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devel/boost-*: update to 1.70.0
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2019-04-12 06:36:31 +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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- Update to 3.3.20190321
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2019-05-20 09:17:29 +00:00 |
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plinkseq
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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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Related to revision 499061 bump ports with USES=fortran to have them
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2019-04-22 13:16:33 +00:00 |
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py-biom-format
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Bump a few PORTREVISIONs after r498529
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2019-04-10 06:18:31 +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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biology/py-bx-python: Update 0.8.2 -> 0.8.4
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2019-06-19 08:08:31 +00:00 |
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py-cutadapt
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biology/py-cutadapt: Upgrade to 2.3
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2019-04-27 01:26:17 +00:00 |
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py-dnaio
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biology/py-dnaio: Read and write FASTQ and FASTA
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2019-03-24 19:40:26 +00:00 |
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py-fastTSNE
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devel/openmp: phase out
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2019-05-08 16:05:53 +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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Bump a few PORTREVISIONs after r498529
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2019-04-10 06:18:31 +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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Bump a few PORTREVISIONs after r498529
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2019-04-10 06:18:31 +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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py-xenaPython
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New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub
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2019-04-12 17:01:10 +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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seqan-apps
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devel/boost-*: update to 1.70.0
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2019-04-12 06:36:31 +00:00 |
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seqan1
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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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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: Remove obsolete pkg-message regarding web interface
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2019-05-10 21:15:42 +00:00 |
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star
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biology/star: Force newer GCC on platforms with GCC 4.2 base
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2019-05-02 00:39:51 +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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Related to revision 499061 bump ports with USES=fortran to have them
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2019-04-22 13:16:33 +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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treekin
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New port: biology/treekin: Efficient computation of RNA folding dynamics
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2019-06-15 20:37:06 +00:00 |
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treepuzzle
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trimadap
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biology/trimadap: Mark only for amd64 and i386
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2019-05-11 00:18:24 +00:00 |
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trimmomatic
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tRNAscan-SE
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biology/tRNAscan-SE: Update to 2.0.3
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2019-06-08 01:31:18 +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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Clean up plist
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2019-04-25 13:25:50 +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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vsearch
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biology/vsearch: Update to 2.13.4
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2019-05-11 13:42:33 +00:00 |
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wise
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Makefile
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New port: biology/treekin: Efficient computation of RNA folding dynamics
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2019-06-15 20:37:06 +00:00 |
47c6c8bc57