Jan Beich 0b055d47f2 devel/boost-*: update to 1.68.0 ... - Switch to C++14 for libboost_system to support C++14 consumers Changes: http://www.boost.org/users/history/version_1_68_0.html PR: 229569 Exp-run by: antoine Differential Revision: https://reviews.freebsd.org/D16165		2018-08-09 06:58:30 +00:00
..
artemis	biology/artemis: Update 9 -> 17.0.1-11	2018-06-11 17:45:56 +00:00
avida	Try to bring some consistency to ports that have x86-specific pieces.	2017-12-21 10:23:19 +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	biology/bedtools: Fix Makefile to respect PREFIX	2018-06-16 17:55:01 +00:00
biococoa	Fix configure options for gnustep-make	2017-12-03 12:23:53 +00:00
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	biology/bowtie2: Upgrade to 2.3.3.1	2017-11-30 02:59:16 +00:00
bwa	Multiple ports:	2018-01-31 01:07:07 +00:00
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	Multiple ports:	2018-01-31 01:07:07 +00:00
chemeq	biology/chemeq: fix build on GCC (taken from dports)	2016-12-18 04:22:26 +00:00
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	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	2018-07-29 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	Return maho@'s ports to the pool after his commit bit expired.	2018-03-11 11:20:43 +00:00
gff2ps
gmap	Multiple ports:	2018-01-31 01:07:07 +00:00
gperiodic	Remove libintl.so.9 compatibility link that was added in r374303 to	2016-12-08 19:52:19 +00:00
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 2.3.13	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	biology/lamarc: Fix build on DF (taken from dports)	2016-12-18 04:34:33 +00:00
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	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	Update devel/readline to 7.0 patch 3	2017-06-27 13:46:53 +00:00
mummer	- Fix installing scripts and support binaries	2017-10-30 02:27:23 +00:00
muscle
ncbi-blast+	Bump PORTREVISION for ports depending on the canonical version of GCC	2018-07-29 22:18:44 +00:00
ncbi-toolkit	Remove libjpeg.so.11 compatibility link that was added in r374303 to	2016-12-08 16:39:11 +00:00
ngs-sdk	Mark as broken on aarch64.	2018-06-25 05:04:46 +00:00
njplot	biology/njplot: Add site in MASTER_SITES because package builders are	2016-11-28 15:19:42 +00:00
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	Fix license information for portgs that use "the same license as Perl".	2017-09-15 08:58:46 +00:00
p5-BioPerl-Run	Update to 1.007002	2017-09-15 19:17:44 +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	[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	devel/boost-*: update to 1.68.0	2018-08-09 06:58:30 +00:00
pbcopper	devel/boost-*: update to 1.68.0	2018-08-09 06:58:30 +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	- Update to 3.697	2018-01-01 08:40:22 +00:00
phyml	biology/phyml: update to v3.3.20180621	2018-06-23 15:53:54 +00:00
plinkseq	Multiple ports:	2018-01-31 01:07:07 +00:00
primer3
protomol	Revision bump of all ports with USE_GL after consolidation of mesa-libs	2017-05-23 05:03:14 +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	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	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 3.1.1 -> 3.2.0	2018-08-09 00:29:50 +00:00
py-orange3-single-cell	biology/py-orange3-single-cell: Update 0.7.0 -> 0.8.0	2018-08-08 23:08:51 +00:00
py-pysam	biology/py-pysam: Update 0.14.1 -> 0.15.0	2018-07-30 19:47:49 +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 1.61	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	- Update to 1.5.1	2017-05-07 15:44:34 +00:00
rubygem-bio	Update to 1.5.1	2017-02-06 23:03:17 +00:00
samtools	biology/samtools: update to 1.9	2018-08-02 19:28:36 +00:00
seaview	biology/seaview: Updatye version 4.6.5=>4.7	2018-07-22 03:22:15 +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	- 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	biology/seqtools: re-try on powerpc* after r449590	2017-12-12 03:38:56 +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	2018-07-29 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	Multiple ports:	2018-01-31 01:07:07 +00:00
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	devel/boost-*: update to 1.68.0	2018-08-09 06:58:30 +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	Remove libintl.so.9 compatibility link that was added in r374303 to	2016-12-08 19:52:19 +00:00
xmolwt	Remove libintl.so.9 compatibility link that was added in r374303 to	2016-12-08 19:52:19 +00:00
Makefile	Regular sorting of categories Makefiles.	2018-08-08 12:26:27 +00:00