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ariadne
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Mark as broken ports with no public distfiles
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2017-10-13 11:14:53 +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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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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- Fix build on 11+
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2017-12-22 12:27:14 +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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Multiple ports:
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2018-01-31 01:07:07 +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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devel/boost-*: update to 1.66.0
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2018-01-18 04:11:02 +00:00 |
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cd-hit
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Multiple ports:
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2018-01-31 01:07:07 +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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clustalw
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consed
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crux
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For ports that are marked BROKEN on armv6, and also fail to build on
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2017-11-30 06:13:34 +00:00 |
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diamond
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biology/diamond: Update to version 0.9.17
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2018-02-01 19:20:07 +00:00 |
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emboss
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fasta
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fasta3
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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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biology/fasttree: update to version 2.1.10
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2017-12-05 03:03:38 +00:00 |
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fastx-toolkit
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Multiple ports:
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2018-01-31 01:07:07 +00:00 |
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fluctuate
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garlic
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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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iolib
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iqtree
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New USES=eigen
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2018-01-02 16:49:24 +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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Multiple ports:
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2018-01-31 01:07:07 +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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molden
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biology/molden: chase another intransparent upstream distfile upgrade.
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2017-11-01 03:48:30 +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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2017-09-10 20:55:38 +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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Multiple ports:
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2018-01-31 01:07:07 +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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Multiple ports:
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2018-01-31 01:07:07 +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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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 3.3.20180129
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2018-02-01 07:26:57 +00:00 |
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plink
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Multiple ports:
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2018-01-31 01:07:07 +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 PORTREVISION for ports depending on the canonical version of GCC
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2017-09-10 20:55:38 +00:00 |
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py-biom-format
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biology/py-biom-format: Add required dependency on math/py-pandas and do
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2017-12-10 03:33:04 +00:00 |
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py-biopython
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Convert Python ports to FLAVORS.
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2017-11-30 15:50:30 +00:00 |
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py-bx-python
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biology/py-bx-python: Update to 0.8.1
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2018-02-10 00:09:56 +00:00 |
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py-cutadapt
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Canonicalize PyPi WWWs:
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2018-02-08 20:18:08 +00:00 |
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py-macs2
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biology/py-macs2: Restrict to python 2.7.
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2017-12-05 02:59:01 +00:00 |
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py-pysam
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biology/py-pysam: Update to 0.14
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2018-02-10 23:01:37 +00:00 |
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pycogent
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- Those ports fail to build with python3
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2017-12-11 16:54:20 +00:00 |
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pyfasta
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Convert Python ports to FLAVORS.
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2017-11-30 15:50:30 +00:00 |
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python-nexus
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Convert Python ports to FLAVORS.
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2017-11-30 15:50:30 +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 4.6.2=>4.6.3
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2018-01-05 17:40:41 +00:00 |
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seqan
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seqan1
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seqan-apps
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devel/boost-*: update to 1.66.0
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2018-01-18 04:11:02 +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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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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ssaha
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Mark as broken ports with no public distfiles
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2017-10-13 11:14:53 +00:00 |
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t_coffee
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2017-09-10 20:55:38 +00:00 |
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tinker
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Fix the context of some patches so that they apply with stricter patch(1)
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2017-11-09 20:45:04 +00:00 |
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treepuzzle
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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 as broken ports with no public distfiles
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2017-10-13 11:14:53 +00:00 |
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ugene
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Update Qt5 ports to 5.9.3.
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2018-01-06 21:30:31 +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/canu: Single molecule sequence assembler
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2017-12-22 01:30:26 +00:00 |
6edd11e5ef