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freebsd-ports/biology
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Gerald Pfeifer a9f015d155 Bump PORTREVISION for ports depending on the canonical version of GCC 
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
2018-12-12 01:35:33 +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
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
biococoa
Update Objective-C LLVM version to 6.0.
2018-09-26 15:23:37 +00:00
bowtie
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
bowtie2
Update devel/tbb to version 2019.1 and bump dependent ports' revisions
2018-10-11 14:47:13 +00:00
bwa
Multiple ports:
2018-01-31 01:07:07 +00:00
canu
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
cd-hit
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
cdbfasta
Multiple ports:
2018-01-31 01:07:07 +00:00
checkm
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
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
Mark QT4 ports/functionality for removal on 2019-03-15
2018-12-02 15:41:47 +00:00
consed
…
cytoscape
biology/cytoscape: Fix license
2018-08-12 06:29:51 +00:00
ddocent
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
Multiple ports:
2018-01-31 01:07:07 +00:00
fastqc
[new port] biology/fastqc: Quality control tool for high throughput sequence data
2017-11-30 22:54:29 +00:00
fasttree
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
fastx-toolkit
biology/fastx-toolkit: Fix build on FreeBSD 12
2018-05-16 15:13:43 +00:00
fluctuate
…
freebayes
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
garlic
Return maho@'s ports to the pool after his commit bit expired.
2018-03-11 11:20:43 +00:00
gatk
devel/gradle: Update to 5.0
2018-12-04 17:53:46 +00:00
gff2ps
…
gmap
Multiple ports:
2018-01-31 01:07:07 +00:00
gperiodic
…
grappa
…
groopm
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
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
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
igv
devel/gradle: Update to 5.0
2018-12-04 17:53:46 +00:00
infernal
Allow building on powerpc64.
2018-09-27 23:02:56 +00:00
iolib
Remove the incorrect typedefs to fix build on tier-2.
2018-11-05 19:45:23 +00:00
iqtree
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
jalview
…
jellyfish
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
kallisto
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
2018-12-12 01:35:33 +00:00
mopac
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
mrbayes
…
mummer
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
muscle
…
ncbi-blast+
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
ncbi-cxx-toolkit
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
ncbi-toolkit
Fix build failure with base GCC because of double typedefs.
2018-11-05 19:47:42 +00:00
ngs-sdk
biology/ngs-sdk: Update 2.9.2 -> 2.9.3
2018-10-18 21:38:21 +00:00
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 PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
p5-TrimGalore
[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming
2017-12-09 13:23:32 +00:00
paml
biology/paml: Set PORTVERSION directly
2018-04-26 15:36:30 +00:00
pbbam
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
pbcopper
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
- Update to 3.697
2018-01-01 08:40:22 +00:00
phyml
Change 4 ports from net/mpich2 to net/mpich
2018-09-22 18:00:24 +00:00
plinkseq
Multiple ports:
2018-01-31 01:07:07 +00:00
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
2018-12-12 01:35:33 +00:00
py-biom-format
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-biopython
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-bx-python
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-loompy
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-macs2
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-orange3-bioinformatics
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-orange3-single-cell
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-pyfaidx
biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2
2018-10-28 04:34:14 +00:00
py-pysam
biology/py-pysam: Update 0.15.0 -> 0.15.1
2018-09-17 17:40:28 +00:00
pycogent
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
pyfasta
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
seqio
- Switch to options helpers
2017-11-26 09:00:21 +00:00
seqtk
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
2018-04-03 20:57:05 +00:00
seqtools
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
sim4
…
slclust
Multiple ports:
2018-01-31 01:07:07 +00:00
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
2018-12-12 01:35:33 +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
2018-12-12 01:35:33 +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
Multiple ports:
2018-01-31 01:07:07 +00:00
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
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
2018-01-11 18:09:00 +00:00
wise
…
xmolwt
Deprecate most glib12 consumers
2018-10-12 09:19:04 +00:00
Makefile
Remove biology/njplot
2018-12-11 15:04:12 +00:00