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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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Try to bring some consistency to ports that have x86-specific pieces.
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2017-12-21 10:23:19 +00:00 |
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babel
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bamtools
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biology/bamtools: API and toolkit for handling BAM files
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2018-03-28 13:26:31 +00:00 |
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bcftools
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Update math/gsl to 2.5
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2018-06-23 08:27:13 +00:00 |
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bedtools
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biology/bedtools: Fix Makefile to respect PREFIX
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2018-06-16 17:55:01 +00:00 |
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biococoa
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Fix configure options for gnustep-make
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2017-12-03 12:23:53 +00:00 |
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blat
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bowtie
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +00:00 |
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bowtie2
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biology/bowtie2: Upgrade to 2.3.3.1
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2017-11-30 02:59:16 +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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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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cd-hit
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +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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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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Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk
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2018-06-28 17:39:53 +00:00 |
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consed
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cytoscape
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New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression
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2018-07-03 08:42:54 +00:00 |
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ddocent
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biology/ddocent: Bash pipeline for RAD sequencing
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2018-04-20 01:34:05 +00:00 |
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diamond
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biology/diamond: Update to version 0.9.22
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2018-05-14 17:17:11 +00:00 |
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emboss
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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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[new port] biology/fastqc: Quality control tool for high throughput sequence data
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2017-11-30 22:54:29 +00:00 |
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fasttree
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Mark the latest version broken on armvX. Note: 2.1.8.3 built ok.
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2018-03-18 13:38:23 +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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fluctuate
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freebayes
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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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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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gff2ps
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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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grappa
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hmmer
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Back out previous commits by jbeich demand.
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2017-12-18 04:28:28 +00:00 |
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htslib
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biology/htslib biology/bcftools biology/samtools: Update to 1.6
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2017-10-25 10:19:50 +00:00 |
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hyphy
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biology/hyphy: Update to version 2.3.13
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2018-05-22 22:55:18 +00:00 |
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igv
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New port: biology/igv: Visualization tool for genomic datasets
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2018-06-25 23:56:00 +00:00 |
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infernal
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Add new port: biology/infernal
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2018-06-06 15:15:18 +00:00 |
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iolib
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Mark various ports broken on mips64 and, where appropriate, mips.
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2018-07-02 00:47:14 +00:00 |
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iqtree
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Mark ports broken on powerpc64, categories a-c.
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2018-06-18 01:48:46 +00:00 |
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jalview
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jellyfish
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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kallisto
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Adjust USES to fix building on gcc-based archs (in particular, powerpc64).
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2018-06-02 19:40:59 +00:00 |
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lagan
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lamarc
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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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- Update to 5.17.0
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2018-06-25 01:37:52 +00:00 |
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linux-foldingathome
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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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biolog/molden: unbreak after at least two intransparent distfile updates
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2018-05-20 21:41:57 +00:00 |
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mopac
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +00:00 |
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mrbayes
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mummer
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- Fix installing scripts and support binaries
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2017-10-30 02:27:23 +00:00 |
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muscle
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ncbi-blast+
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Mark as broken on powerpc64. The entire, unhelpful, error message is:
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2018-06-03 11:14:53 +00:00 |
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ncbi-toolkit
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ngs-sdk
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Mark as broken on aarch64.
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2018-06-25 05:04:46 +00:00 |
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njplot
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p5-AcePerl
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-ASN1-EntrezGene
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-Coordinate
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-Das
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-Das-Lite
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-FeatureIO
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-GFF3
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-Glite
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-Graphics
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-MAGETAB
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-NEXUS
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-Phylo
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-Bio-SCF
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Update WWW
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2018-05-27 20:15:16 +00:00 |
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p5-BioPerl
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Fix license information for portgs that use "the same license as Perl".
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2017-09-15 08:58:46 +00:00 |
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p5-BioPerl-Run
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Update to 1.007002
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2017-09-15 19:17:44 +00:00 |
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p5-transdecoder
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +00:00 |
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p5-TrimGalore
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[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming
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2017-12-09 13:23:32 +00:00 |
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paml
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biology/paml: Set PORTVERSION directly
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2018-04-26 15:36:30 +00:00 |
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pbbam
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biology/pbbam: PacBio BAM C++ library, with SWIG bindings
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2018-04-23 16:08:21 +00:00 |
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pbcopper
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biology/pbcopper: Core C++ library for Pacific Biosciences tools
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2018-04-23 16:23:53 +00:00 |
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pbseqan
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biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn
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2018-04-21 17:21:30 +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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phred
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phylip
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- Update to 3.697
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2018-01-01 08:40:22 +00:00 |
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phyml
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biology/phyml: update to v3.3.20180621
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2018-06-23 15:53:54 +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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protomol
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psi88
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +00:00 |
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py-biom-format
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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-biopython
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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-bx-python
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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-cutadapt
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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-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-macs2
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +00:00 |
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py-orange3-bioinformatics
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New port: biology/py-orange3-bioinformatics: Orange add-on providing common functionality for bioinformatics
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2018-06-14 06:25:21 +00:00 |
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py-pysam
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Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
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2018-04-25 16:42:37 +00:00 |
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pycogent
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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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pyfasta
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +00:00 |
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python-nexus
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- Update to 1.61
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2018-04-01 11:52:08 +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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samtools
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Add a USES=python:env, that will not add a dependency on Python.
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2017-12-04 15:27:29 +00:00 |
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seaview
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biology/seaview: Update version 4.6.3=>4.6.5
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2018-04-24 12:31:32 +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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Mark as broken on powerpc64 pending fix for PR 199603.
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2018-06-18 19:14:48 +00:00 |
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seqio
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- Switch to options helpers
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2017-11-26 09:00:21 +00:00 |
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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: re-try on powerpc* after r449590
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2017-12-12 03:38:56 +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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Adjust USES to fix builds on gcc-based architectures.
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2018-06-18 19:03:03 +00:00 |
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t_coffee
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +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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tinker
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Bump PORTREVISIONs of all users of math/mpc that we just updated to
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2018-03-10 17:46:04 +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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Mark BROKEN: missing plist
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2018-06-29 12:43:19 +00:00 |
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ugene
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Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk
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2018-06-28 17:39:53 +00:00 |
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unanimity
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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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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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Multiple ports:
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2018-01-31 01:07:07 +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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xmolwt
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Makefile
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New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression
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2018-07-03 08:42:54 +00:00 |
