.. |
artemis
|
biology/artemis: Update 9 -> 17.0.1-11
|
2018-06-11 17:45:56 +00:00 |
avida
|
|
|
babel
|
|
|
bamtools
|
|
|
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
|
|
|
blat
|
|
|
bowtie
|
|
|
bowtie2
|
|
|
bwa
|
|
|
canu
|
Mark as broken on aarch64, and, where appropriate, armvX.
|
2018-06-21 23:52:37 +00:00 |
cd-hit
|
|
|
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
|
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
|
|
|
diamond
|
biology/diamond: Update to version 0.9.22
|
2018-05-14 17:17:11 +00:00 |
emboss
|
|
|
fasta
|
|
|
fasta3
|
|
|
fastahack
|
|
|
fastdnaml
|
|
|
fastool
|
|
|
fastqc
|
|
|
fasttree
|
|
|
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
|
|
|
gff2ps
|
|
|
gmap
|
|
|
gperiodic
|
|
|
grappa
|
|
|
hmmer
|
|
|
htslib
|
|
|
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
|
Mark ports broken on powerpc64, categories a-c.
|
2018-06-18 01:48:46 +00:00 |
jalview
|
|
|
jellyfish
|
|
|
kallisto
|
Adjust USES to fix building on gcc-based archs (in particular, powerpc64).
|
2018-06-02 19:40:59 +00:00 |
lagan
|
|
|
lamarc
|
|
|
libgtextutils
|
|
|
libsbml
|
- Update to 5.17.0
|
2018-06-25 01:37:52 +00:00 |
linux-foldingathome
|
|
|
mafft
|
|
|
mapm3
|
|
|
migrate
|
|
|
molden
|
biolog/molden: unbreak after at least two intransparent distfile updates
|
2018-05-20 21:41:57 +00:00 |
mopac
|
|
|
mrbayes
|
|
|
mummer
|
|
|
muscle
|
|
|
ncbi-blast+
|
Mark as broken on powerpc64. The entire, unhelpful, error message is:
|
2018-06-03 11:14:53 +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
|
|
|
p5-BioPerl-Run
|
|
|
p5-transdecoder
|
|
|
p5-TrimGalore
|
|
|
paml
|
biology/paml: Set PORTVERSION directly
|
2018-04-26 15:36:30 +00:00 |
pbbam
|
|
|
pbcopper
|
biology/pbcopper: Core C++ library for Pacific Biosciences tools
|
2018-04-23 16:23:53 +00:00 |
pbseqan
|
|
|
pear-merger
|
Mark as broken on aarch64, and, where appropriate, armvX.
|
2018-06-21 23:52:37 +00:00 |
phrap
|
|
|
phred
|
|
|
phylip
|
|
|
phyml
|
biology/phyml: update to v3.3.20180621
|
2018-06-23 15:53:54 +00:00 |
plinkseq
|
|
|
primer3
|
|
|
protomol
|
|
|
psi88
|
|
|
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
|
|
|
py-orange3-bioinformatics
|
New port: biology/py-orange3-bioinformatics: Orange add-on providing common functionality for bioinformatics
|
2018-06-14 06:25:21 +00:00 |
py-pysam
|
Switch all pypi.python.org WWWs to a new PyPi home pypi.org where
|
2018-04-25 16:42:37 +00:00 |
pycogent
|
Use PY_FLAVOR for dependencies.
|
2018-06-20 17:05:41 +00:00 |
pyfasta
|
|
|
python-nexus
|
|
|
rainbow
|
|
|
recombine
|
|
|
ruby-bio
|
|
|
rubygem-bio
|
|
|
samtools
|
|
|
seaview
|
biology/seaview: Update version 4.6.3=>4.6.5
|
2018-04-24 12:31:32 +00:00 |
seqan
|
|
|
seqan1
|
|
|
seqan-apps
|
Mark as broken on powerpc64 pending fix for PR 199603.
|
2018-06-18 19:14:48 +00:00 |
seqio
|
|
|
seqtk
|
|
|
seqtools
|
|
|
sim4
|
|
|
slclust
|
|
|
smithwaterman
|
|
|
stacks
|
Adjust USES to fix builds on gcc-based architectures.
|
2018-06-18 19:03:03 +00:00 |
t_coffee
|
|
|
tabixpp
|
|
|
tinker
|
|
|
treepuzzle
|
|
|
trimadap
|
Mark as broken on aarch64, and, where appropriate, armvX.
|
2018-06-21 23:52:37 +00:00 |
trimmomatic
|
|
|
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
|
|
|
velvet
|
|
|
wise
|
|
|
xmolwt
|
|
|
Makefile
|
New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression
|
2018-07-03 08:42:54 +00:00 |