Mark Linimon ff4e0e08dd Fix build with tier-2 arches. ... PR: 231448 Submitted by: Piotr Kubaj Approved by: maintainer		2018-10-28 08:58:00 +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
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
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
diamond
emboss
exonerate	New port: biology/exonerate: Generic tool for sequence alignment	2018-07-13 07:02:16 +00:00
fasta
fasta3
fastahack
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
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
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
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
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	biology/p5-transdecoder: Upgrade to 5.4.0	2018-10-23 12:51:20 +00:00
p5-TrimGalore
paml
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
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
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	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	Use PY_FLAVOR for dependencies.	2018-06-20 17:05:41 +00:00
pyfasta
python-nexus	- Update to 1.63	2018-09-22 08:54:58 +00:00
rainbow
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
seqan1
seqan-apps	devel/boost-*: update to 1.68.0	2018-08-09 06:58:30 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks	Fix build with tier-2 arches.	2018-10-28 08:58:00 +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
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