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09f9633cb6
freebsd-ports/biology
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Gerald Pfeifer 09f9633cb6 Bump PORTREVISION for ports depending on the canonical version of GCC 
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
2018-07-29 22:18:44 +00:00
..
artemis biology/artemis: Update 9 -> 17.0.1-11 2018-06-11 17:45:56 +00:00
avida
babel
bamtools
bcftools Update math/gsl to 2.5 2018-06-23 08:27:13 +00:00
bedtools biology/bedtools: Fix Makefile to respect PREFIX 2018-06-16 17:55:01 +00:00
biococoa
blat Deprecate unmaintained ports under the NONE license 2018-07-13 09:56:57 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
bowtie2
bwa
canu Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +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 New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression 2018-07-03 08:42:54 +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 Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
garlic
gff2ps
gmap
gperiodic
grappa
hmmer biology/hmmer: update to 3.2.1 2018-07-11 15:15:03 +00:00
htslib biology/htslib: Update 1.6 -> 1.8 2018-07-16 18:11:44 +00:00
hyphy biology/hyphy: Update to version 2.3.13 2018-05-22 22:55:18 +00:00
igv New port: biology/igv: Visualization tool for genomic datasets 2018-06-25 23:56:00 +00:00
infernal Add new port: biology/infernal 2018-06-06 15:15:18 +00:00
iolib Mark various ports broken on mips64 and, where appropriate, mips. 2018-07-02 00:47:14 +00:00
iqtree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
kallisto Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
lagan
lamarc
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml - Update to 5.17.0 2018-06-25 01:37:52 +00:00
linux-foldingathome biology/linux-foldingathome: reset maintainer by request 2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate
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-toolkit
ngs-sdk Mark as broken on aarch64. 2018-06-25 05:04:46 +00:00
njplot
p5-AcePerl Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-ASN1-EntrezGene Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Coordinate Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Das Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Das-Lite Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-FeatureIO Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-GFF3 Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Glite Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Graphics Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-MAGETAB Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-NEXUS Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Phylo Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-SCF Update WWW 2018-05-27 20:15:16 +00:00
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml biology/paml: Set PORTVERSION directly 2018-04-26 15:36:30 +00:00
pbbam biology/pbbam: PacBio BAM C++ library, with SWIG bindings 2018-04-23 16:08:21 +00:00
pbcopper biology/pbcopper: Core C++ library for Pacific Biosciences tools 2018-04-23 16:23:53 +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
phred
phylip
phyml biology/phyml: update to v3.3.20180621 2018-06-23 15:53:54 +00:00
plinkseq
primer3
protomol
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
py-biom-format Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-biopython Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-bx-python Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-cutadapt Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-macs2
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.1.0 -> 3.1.1 2018-07-12 20:09:38 +00:00
py-pysam Switch all pypi.python.org WWWs to a new PyPi home pypi.org where 2018-04-25 16:42:37 +00:00
pycogent Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
pyfasta
python-nexus - Update to 1.61 2018-04-01 11:52:08 +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
samtools
seaview biology/seaview: Updatye version 4.6.5=>4.7 2018-07-22 03:22:15 +00:00
seqan
seqan1
seqan-apps Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +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
tinker Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
treepuzzle
trimadap Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
trimmomatic
tRNAscan-SE Mark BROKEN: missing plist 2018-06-29 12:43:19 +00:00
ugene Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk 2018-06-28 17:39:53 +00:00
unanimity Mark these ports as broken on aarch64. 2018-06-22 00:03:08 +00:00
vcflib Mark these ports as broken on aarch64. 2018-06-22 00:03:08 +00:00
vcftools
velvet
wise
xmolwt
Makefile New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00