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ports/biology
History
Yuri Victorovich f5af0f0e92 biology/py-pysam: Update 0.14.1 -> 0.15.0 
Port changes:
* Remove stripping: done by the project now
* Update WWW

Reported by:	portscout
2018-07-30 19:47:49 +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
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
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
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
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 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
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
…
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
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
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
- 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 3.1.0 -> 3.1.1
2018-07-12 20:09:38 +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
Add a USES=python:env, that will not add a dependency on Python.
2017-12-04 15:27:29 +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
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-07-29 22:18:44 +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
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
Multiple ports:
2018-01-31 01:07:07 +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
New port: biology/exonerate: Generic tool for sequence alignment
2018-07-13 07:02:16 +00:00