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freebsd-ports/biology
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Joseph Mingrone 6c672c455f biology/hyphy: Update to version 2.3.14.16 
This pulls in fixes after the 2.3.14 release.

Upstream changes for version 2.3.14:
https://github.com/veg/hyphy/releases/tag/2.3.14

Subsequent fixes:
https://github.com/veg/hyphy/commit/1ecac31
https://github.com/veg/hyphy/commit/bec6833
https://github.com/veg/hyphy/commit/9847438
https://github.com/veg/hyphy/commit/02dcedd
https://github.com/veg/hyphy/commit/8f44d3c
https://github.com/veg/hyphy/commit/5297c30
https://github.com/veg/hyphy/commit/3d88d3e
2018-10-20 12:21:15 +00:00
..
artemis biology/artemis: Update 9 -> 17.0.1-11 2018-06-11 17:45:56 +00:00
avida biology/avida: Fix build with Clang 6 2018-08-25 03:22:18 +00:00
babel
bamtools biology/bamtools: API and toolkit for handling BAM files 2018-03-28 13:26:31 +00:00
bcftools biology/bcftools: update to 1.9 2018-08-02 19:30:57 +00:00
bedtools Fix build on gcc-based archs by updating USES. 2018-09-22 05:30:31 +00:00
biococoa Update Objective-C LLVM version to 6.0. 2018-09-26 15:23:37 +00:00
bowtie Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
bowtie2 Update devel/tbb to version 2019.1 and bump dependent ports' revisions 2018-10-11 14:47:13 +00:00
bwa
canu devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
cdbfasta
chemeq
clustal-omega biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw 2018-05-21 22:15:26 +00:00
clustalw biology/clustalw: Fix license, take maintainership 2018-05-21 01:13:40 +00:00
clustalx Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk 2018-06-28 17:39:53 +00:00
consed
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +00:00
ddocent biology/ddocent: Bash pipeline for RAD sequencing 2018-04-20 01:34:05 +00:00
diamond biology/diamond: Update to version 0.9.22 2018-05-14 17:17:11 +00:00
emboss
exonerate New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00
fasta
fasta3
fastahack biology/fastahack: Utility for indexing and sequence extraction from FASTA files 2018-04-16 14:50:46 +00:00
fastdnaml
fastool
fastqc
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
fastx-toolkit biology/fastx-toolkit: Fix build on FreeBSD 12 2018-05-16 15:13:43 +00:00
fluctuate
freebayes Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based 2018-09-18 09:28:34 +00:00
garlic Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
gff2ps
gmap
gperiodic
grappa
hmmer biology/hmmer: update to 3.2.1 2018-07-11 15:15:03 +00:00
htslib biology/htslib: update to 1.9 2018-08-02 19:27:13 +00:00
hyphy biology/hyphy: Update to version 2.3.14.16 2018-10-20 12:21:15 +00:00
igv New port: biology/igv: Visualization tool for genomic datasets 2018-06-25 23:56:00 +00:00
infernal Allow building on powerpc64. 2018-09-27 23:02:56 +00:00
iolib - Update to 1-14-10 2018-09-28 18:47:49 +00:00
iqtree biology/iqtree: Update to version 1.6.7.1 2018-10-16 13:49:54 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
kallisto Update science/hdf5 to 1.10.2 2018-09-05 22:05:23 +00:00
lagan
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml biology/libsbml: Fix build with Clang 6 2018-08-25 03:31:43 +00:00
linux-foldingathome biology/linux-foldingathome: reset maintainer by request 2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate Mark broken on armvX and mips. 2018-03-18 13:48:07 +00:00
molden Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
mrbayes
mummer
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
ncbi-cxx-toolkit New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkit 2018-10-08 07:54:49 +00:00
ncbi-toolkit biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06 2018-10-07 18:29:16 +00:00
ngs-sdk biology/ngs-sdk: Update 2.9.2 -> 2.9.3 2018-10-18 21:38:21 +00:00
njplot
p5-AcePerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene Update to 1.73 2018-10-10 10:23:10 +00:00
p5-Bio-Coordinate Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das-Lite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-FeatureIO Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-GFF3 Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Glite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Graphics Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-MAGETAB Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-NEXUS Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Phylo Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-SCF Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-BioPerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-BioPerl-Run Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-transdecoder Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
p5-TrimGalore
paml biology/paml: Set PORTVERSION directly 2018-04-26 15:36:30 +00:00
pbbam More precisely specify USES=compiler to fix build on gcc-based 2018-09-18 08:14:23 +00:00
pbcopper More precisely specify USES=compiler to fix build on gcc-based 2018-09-18 08:14:23 +00:00
pbseqan biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn 2018-04-21 17:21:30 +00:00
pear-merger Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
phrap Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phred Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phylip
phyml Change 4 ports from net/mpich2 to net/mpich 2018-09-22 18:00:24 +00:00
plinkseq
primer3 biology/primer3: Fix build with Clang 6 2018-08-25 03:35:46 +00:00
protomol biology/protomol: Fix doubled USES overwriting the old value 2018-08-25 03:47:25 +00:00
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
py-biom-format biology/py-biom-format: Update to version 2.1.7 2018-10-06 15:28:01 +00:00
py-biopython - Update to 1.72 2018-08-24 00:12:38 +00:00
py-bx-python biology/py-bx-python: Update 0.8.1 -> 0.8.2 2018-08-26 09:50:41 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 1.18 2018-09-20 14:10:52 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-gffutils New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +00:00
py-gtfparse New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) files 2018-10-19 02:03:40 +00:00
py-loompy biology/py-loompy: Update 2.0.14 -> 2.0.15 2018-10-19 05:01:45 +00:00
py-macs2 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2 2018-10-14 03:22:49 +00:00
py-orange3-single-cell biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2 2018-10-17 07:31:34 +00:00
py-pyfaidx New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subsequences 2018-10-19 02:05:37 +00:00
py-pysam biology/py-pysam: Update 0.15.0 -> 0.15.1 2018-09-17 17:40:28 +00:00
pycogent Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
pyfasta Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
python-nexus - Update to 1.63 2018-09-22 08:54:58 +00:00
rainbow biology/rainbow: Efficient clustering and assembling of short reads 2018-04-02 16:50:46 +00:00
recombine
ruby-bio
rubygem-bio Update to 1.5.2 2018-09-21 18:08:24 +00:00
samtools biology/samtools: update to 1.9 2018-08-02 19:28:36 +00:00
seaview biology/seaview: Fix build with Clang 6 2018-09-08 09:01:35 +00:00
seqan biology/seqan-apps, biology/seqan: Update to 2.4.0 2018-03-10 06:21:37 +00:00
seqan1
seqan-apps devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
seqio
seqtk biology/seqtk: Tool for processing sequences in FASTA/FASTQ format 2018-04-03 20:57:05 +00:00
seqtools
sim4
slclust
smithwaterman biology/smithwaterman: Smith-waterman-gotoh alignment algorithm 2018-04-15 17:45:52 +00:00
stacks biology/stacks: Enable OpenMP (oversight in previous commit) 2018-09-01 14:14:11 +00:00
stringtie New port: biology/stringtie: Transcript assembly and quantification for RNA-seq 2018-07-11 21:32:39 +00:00
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +00:00
treepuzzle
trimadap Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
trimmomatic
tRNAscan-SE - Unbreak by adding missing pkg-plist 2018-09-28 00:12:48 +00:00
ugene Update to 1.31.0 2018-09-02 20:47:15 +00:00
unanimity More precisely specify USES=compiler to fix build on gcc-based 2018-09-18 08:14:23 +00:00
vcflib Mark these ports as broken on aarch64. 2018-06-22 00:03:08 +00:00
vcftools biology/vcftools: Update to 0.1.16, a security release 2018-08-04 01:29:29 +00:00
velvet
wise
xmolwt Deprecate most glib12 consumers 2018-10-12 09:19:04 +00:00
Makefile New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +00:00