Sunpoet Po-Chuan Hsieh 91c3078096 Update science/hdf5 to 1.10.4 ... - Bump PORTREVISION of dependent ports for shlib change Changes: https://portal.hdfgroup.org/display/support/HDF5%201.10.4#releasenotes PR: 233070 Submitted by: wen		2019-01-05 22:46:53 +00:00
..
artemis	biology/artemis: Update 9 -> 17.0.1-11	2018-06-11 17:45:56 +00:00
avida	Change cmake default behaviour to outsource.	2018-12-25 20:25:39 +00:00
babel
bamtools	Change cmake default behaviour to outsource.	2018-12-25 20:25:39 +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
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
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 0.9.24	2018-12-31 19:00:00 +00:00
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	2018-12-12 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
gatk	devel/gradle: Update to 5.0	2018-12-04 17:53:46 +00:00
gff2ps	biology/gff2ps: update 0.98d to 0.98l	2018-12-19 17:34:29 +00:00
gmap
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	Change cmake default behaviour to outsource.	2018-12-25 20:25:39 +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	biology/iqtree: switch to outsource cmake build	2018-12-27 18:34:44 +00:00
jalview
jellyfish	Bump PORTREVISION for ports depending on the canonical version of GCC	2018-12-12 01:35:33 +00:00
kallisto	Update science/hdf5 to 1.10.4	2019-01-05 22:46:53 +00:00
lagan
lamarc	biology/lamarc: Fix build with Clang 6	2018-08-25 03:13:37 +00:00
libgtextutils
libsbml	Change cmake default behaviour to outsource.	2018-12-25 20:25:39 +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	2018-12-12 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+	biology/ncbi-blast+: Upgrade to 2.8.1	2019-01-01 19:55:44 +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
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
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	2018-12-12 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	- Update to 1.73	2018-12-22 04:54:51 +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-fastTSNE	New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE	2018-12-15 08:58:05 +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
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	Change cmake default behaviour to outsource.	2018-12-25 20:25:39 +00:00
seqio
seqtk
seqtools	Bump PORTREVISION for ports depending on the canonical version of GCC	2018-12-12 01:35:33 +00:00
sim4
slclust
smithwaterman
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
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 Qt5 to 5.12.0	2018-12-16 14:49:16 +00:00
unanimity	Change cmake default behaviour to outsource.	2018-12-25 20:25:39 +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
Makefile	Remove expired ports:	2018-12-21 13:19:02 +00:00