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ariadne
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Deprecate ports broken for more than 6 months
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2018-05-05 10:49:36 +00:00 |
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artemis
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Remove dead master sites
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2017-10-13 11:14:32 +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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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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bedtools
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biology/bedtools: Upgrade to 2.27.1
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2018-04-19 16:44:59 +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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- Update WWW
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2017-06-10 09:01:19 +00:00 |
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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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biology/canu: Upgrade to 1.7 release
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2018-04-26 04:16:15 +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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biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI
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2018-05-21 20:56:17 +00:00 |
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consed
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crux
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Deprecate ports broken for more than 6 months
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2018-05-05 10:49:36 +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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biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping
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2018-04-20 00:07:27 +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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iolib
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iqtree
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biology/iqtree: Update to version 1.6.5
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2018-05-11 16:57:09 +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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[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data
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2017-12-02 20:44:28 +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 5.16.0
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2018-01-01 08:24:53 +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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Update devel/readline to 7.0 patch 3
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2017-06-27 13:46:53 +00:00 |
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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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biology/ncbi-blast+: Upgrade to 2.7.1
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2018-03-27 18:04:21 +00:00 |
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ncbi-toolkit
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njplot
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p5-AcePerl
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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-Bio-ASN1-EntrezGene
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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-Bio-Coordinate
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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-Bio-Das
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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-Bio-Das-Lite
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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-Bio-FeatureIO
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Add p5-Bio-FeatureIO 1.6.905
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2017-09-15 19:17:17 +00:00 |
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p5-Bio-GFF3
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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-Bio-Glite
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p5-Bio-Graphics
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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-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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Update to 2.0.1
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2017-12-26 23:20:28 +00:00 |
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p5-Bio-SCF
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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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biology/pear-merger: Memory-efficient and accurate paired-end read merger
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2018-04-04 17:21:39 +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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- Update to 3.3.20180214
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2018-05-15 03:17:54 +00:00 |
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plink
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Deprecate ports broken for more than 6 months
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2018-05-05 10:49:36 +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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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-biopython
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biology/py-biopython: Unbreak on python3; Add license
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2018-05-13 22:30:00 +00:00 |
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py-bx-python
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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-cutadapt
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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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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-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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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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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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devel/boost-*: update to 1.67.0
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2018-04-18 13:57:42 +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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ssaha
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Deprecate ports broken for more than 6 months
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2018-05-05 10:49:36 +00:00 |
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stacks
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biology/stacks: Software pipeline for building loci from short-read sequences
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2018-03-31 13:16:05 +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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biology/trimadap: Trim adapter sequences from Illumina data
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2018-04-03 18:23:54 +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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Deprecate ports broken for more than 6 months
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2018-05-05 10:49:36 +00:00 |
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ugene
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Add upstream patch to fix the build with Qt 5.10.
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2018-05-15 18:51:51 +00:00 |
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unanimity
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biology/unanimity: Pacific Biosciences consensus library and applications
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2018-04-24 14:16:46 +00:00 |
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vcflib
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biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files
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2018-04-17 03:11:39 +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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biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw
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2018-05-21 22:15:26 +00:00 |
