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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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biology/avida: Fix build with Clang 6
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2018-08-25 03:22:18 +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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biology/bcftools: update to 1.9
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2018-08-02 19:30:57 +00:00 |
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bedtools
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Fix build on gcc-based archs by updating USES.
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2018-09-22 05:30:31 +00:00 |
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biococoa
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Update Objective-C LLVM version to 6.0.
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2018-09-26 15:23:37 +00:00 |
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bowtie
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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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bowtie2
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Update devel/tbb to version 2019 and bump dependent port's revisions
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2018-10-04 10:03:59 +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 1.68.0
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2018-08-09 06:58:30 +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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2018-07-29 22:18:44 +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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biology/cytoscape: Fix license
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2018-08-12 06:29:51 +00:00 |
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ddocent
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biology/ddocent: 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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exonerate
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New port: biology/exonerate: Generic tool for sequence alignment
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2018-07-13 07:02:16 +00:00 |
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fasta
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fasta3
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fastahack
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biology/fastahack: Utility for indexing and sequence extraction from FASTA files
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2018-04-16 14:50:46 +00:00 |
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fastdnaml
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fastool
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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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-07-29 22:18:44 +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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Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based
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2018-09-18 09:28:34 +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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biology/hmmer: update to 3.2.1
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2018-07-11 15:15:03 +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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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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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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- Update to 1-14-10
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2018-09-28 18:47:49 +00:00 |
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iqtree
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biology/iqtree: Update to version 1.6.7
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2018-08-27 01:20:28 +00:00 |
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jalview
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jellyfish
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-07-29 22:18:44 +00:00 |
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kallisto
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Update science/hdf5 to 1.10.2
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2018-09-05 22:05:23 +00:00 |
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lagan
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lamarc
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biology/lamarc: Fix build with Clang 6
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2018-08-25 03:13:37 +00:00 |
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libgtextutils
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biology/libgtextutils: Unbreak for FreeBSD 12
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2018-03-29 15:41:07 +00:00 |
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libsbml
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biology/libsbml: Fix build with Clang 6
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2018-08-25 03:31:43 +00:00 |
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linux-foldingathome
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biology/linux-foldingathome: reset maintainer by request
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2018-07-27 02:19:43 +00:00 |
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mafft
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mapm3
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migrate
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Mark broken on armvX and mips.
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2018-03-18 13:48:07 +00:00 |
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molden
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-07-29 22:18:44 +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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2018-07-29 22:18:44 +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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-07-29 22:18:44 +00:00 |
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ncbi-cxx-toolkit
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New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkit
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2018-10-08 07:54:49 +00:00 |
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ncbi-toolkit
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biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06
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2018-10-07 18:29:16 +00:00 |
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ngs-sdk
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biology/ngs-sdk: Update 2.9.1 -> 2.9.2
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2018-09-19 18:09:37 +00:00 |
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njplot
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p5-AcePerl
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-ASN1-EntrezGene
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Update to 1.73
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2018-10-10 10:23:10 +00:00 |
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p5-Bio-Coordinate
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Fix every instance of RUN_DEPENDS:=${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 every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-NEXUS
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Fix every instance of RUN_DEPENDS:=${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:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-Bio-SCF
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-BioPerl
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-BioPerl-Run
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Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
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2018-10-06 13:06:42 +00:00 |
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p5-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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More precisely specify USES=compiler to fix build on gcc-based
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2018-09-18 08:14:23 +00:00 |
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pbcopper
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More precisely specify USES=compiler to fix build on gcc-based
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2018-09-18 08:14:23 +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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Add DOCS options to ports that should have one.
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2018-09-10 13:14:50 +00:00 |
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phred
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Add DOCS options to ports that should have one.
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2018-09-10 13:14:50 +00:00 |
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phylip
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- 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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Change 4 ports from net/mpich2 to net/mpich
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2018-09-22 18:00:24 +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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biology/primer3: Fix build with Clang 6
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2018-08-25 03:35:46 +00:00 |
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protomol
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biology/protomol: Fix doubled USES overwriting the old value
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2018-08-25 03:47:25 +00:00 |
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psi88
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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-07-29 22:18:44 +00:00 |
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py-biom-format
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biology/py-biom-format: Update to version 2.1.7
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2018-10-06 15:28:01 +00:00 |
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py-biopython
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- Update to 1.72
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2018-08-24 00:12:38 +00:00 |
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py-bx-python
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biology/py-bx-python: Update 0.8.1 -> 0.8.2
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2018-08-26 09:50:41 +00:00 |
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py-cutadapt
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biology/py-cutadapt: Upgrade to 1.18
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2018-09-20 14:10:52 +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-loompy
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New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data
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2018-09-21 08:04:50 +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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biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0
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2018-08-09 00:29:50 +00:00 |
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py-orange3-single-cell
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biology/py-orange3-single-cell: Update 0.7.0 -> 0.8.0
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2018-08-08 23:08:51 +00:00 |
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py-pysam
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biology/py-pysam: Update 0.15.0 -> 0.15.1
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2018-09-17 17:40:28 +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 1.63
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2018-09-22 08:54:58 +00:00 |
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rainbow
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biology/rainbow: Efficient clustering and assembling of short reads
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2018-04-02 16:50:46 +00:00 |
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recombine
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ruby-bio
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rubygem-bio
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Update to 1.5.2
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2018-09-21 18:08:24 +00:00 |
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samtools
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biology/samtools: update to 1.9
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2018-08-02 19:28:36 +00:00 |
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seaview
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biology/seaview: Fix build with Clang 6
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2018-09-08 09:01:35 +00:00 |
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seqan
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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 1.68.0
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2018-08-09 06:58:30 +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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biology/stacks: Enable OpenMP (oversight in previous commit)
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2018-09-01 14:14:11 +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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Bump PORTREVISION for ports depending on the canonical version of GCC
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2018-07-29 22:18:44 +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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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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- Unbreak by adding missing pkg-plist
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2018-09-28 00:12:48 +00:00 |
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ugene
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Update to 1.31.0
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2018-09-02 20:47:15 +00:00 |
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unanimity
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More precisely specify USES=compiler to fix build on gcc-based
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2018-09-18 08:14:23 +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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- 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/ncbi-cxx-toolkit: NCBI C++ Toolkit
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2018-10-08 07:54:49 +00:00 |
