| .. |
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abyss
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devel/openmp: update to 9.0.0
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2019-09-21 18:59:57 +00:00 |
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artemis
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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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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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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 2.29.0
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2019-09-13 13:21:59 +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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devel/boost-*: update to 1.71.0
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2019-08-19 15:35:27 +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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2019-07-26 20:46:53 +00:00 |
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bowtie2
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Update devel/tbb to 2019.8 and bump dependent ports' revisions
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2019-09-25 10:03:49 +00:00 |
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bwa
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canu
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biology/canu: Upgrade to 1.9
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2019-11-08 14:03:15 +00:00 |
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cd-hit
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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cdbfasta
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checkm
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biology/checkm: Update 1.0.17 -> 1.0.18
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2019-08-19 08:25:29 +00:00 |
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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 1.71.0
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2019-08-19 15:35:27 +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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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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 1.71.0
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2019-08-19 15:35:27 +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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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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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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fasta3
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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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fastahack
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biology/fastahack: Upgrade to 1.0.0
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2019-10-06 21:34:32 +00:00 |
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fastdnaml
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fastool
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fastp
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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fastqc
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biology/fastqc: Upgrade to 0.11.8
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2019-09-21 02:44:54 +00:00 |
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fasttree
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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fastx-toolkit
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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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2019-07-26 20:46:53 +00:00 |
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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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Create devel/gradle5 in preparation of devel/gradle update
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2019-11-20 09:51:43 +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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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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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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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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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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haplohseq
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biology/haplohseq: Switch to distfile with example data
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2019-11-17 15:00:13 +00:00 |
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hhsuite
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devel/openmp: update to 9.0.0
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2019-09-21 18:59:57 +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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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +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 1.6.12
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2019-08-27 01:19:11 +00:00 |
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jalview
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jellyfish
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Drop C++11 workaround for GCC < 6 after r449590
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2019-09-14 22:01:13 +00:00 |
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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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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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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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libbigwig
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New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)
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2019-07-11 17:05:22 +00:00 |
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libgtextutils
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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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mafft
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mapm3
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migrate
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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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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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mothur
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biology/mothur: Update 1.42.3 -> 1.43.0
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2019-10-05 17:04:42 +00:00 |
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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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muscle
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ncbi-blast+
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +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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biologi/ncbi-toolkit: Remove dependency on libXp
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2019-09-28 10:52:57 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Update 2.9.6 -> 2.10.0
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2019-08-31 15:09:47 +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 1.007006 (1.7.6)
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2019-09-07 22:44:02 +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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2019-07-26 20:46:53 +00:00 |
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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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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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pbcopper
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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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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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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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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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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: update to 3.3.20190909
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2019-09-10 21:04:16 +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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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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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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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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devel/openmp: update to 9.0.0
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2019-09-21 18:59:57 +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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2019-07-26 20:46:53 +00:00 |
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py-loompy
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +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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2019-07-26 20:46:53 +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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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py-orange3-single-cell
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +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 0.15.2 -> 0.15.3
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2019-08-31 15:49:18 +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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2019-07-26 20:46:53 +00:00 |
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pyfasta
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +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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recombine
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Fix after gets(3) retirement using gets_s(3).
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2019-09-02 05:00:43 +00:00 |
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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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Convert to UCL & cleanup pkg-message (categories a-c)
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2019-08-13 16:00:39 +00:00 |
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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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Fix some misspelled or duplicated LICENSE_*
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2019-09-17 19:21:45 +00:00 |
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seqan-apps
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devel/boost-*: update to 1.71.0
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2019-08-19 15:35:27 +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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +00:00 |
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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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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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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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biology/tophat: Fast splice junction mapper for RNA-Seq reads
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2019-09-27 00:49:48 +00:00 |
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treekin
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2019-07-26 20:46:53 +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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biology/trimmomatic: Upgrade to 0.39
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2019-09-14 14:45:49 +00:00 |
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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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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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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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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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viennarna
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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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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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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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Remove expired ports:
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2019-10-16 15:29:32 +00:00 |
795a4fecb2