| .. |
|
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
|
biology/bedtools: Fix Makefile to respect PREFIX
|
2018-06-16 17:55:01 +00:00 |
|
biococoa
|
|
|
|
bowtie
|
Add DOCS options to ports that should have one.
|
2018-09-10 13:14:50 +00:00 |
|
bowtie2
|
|
|
|
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
|
|
|
|
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
|
|
|
|
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
|
biology/iqtree: Update to version 1.6.7
|
2018-08-27 01:20:28 +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-toolkit
|
|
|
|
ngs-sdk
|
biology/ngs-sdk: Update 2.9.1 -> 2.9.2
|
2018-09-19 18:09:37 +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
|
|
|
|
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
|
biology/phyml: update to v3.3.20180621
|
2018-06-23 15:53:54 +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
|
Use PY_FLAVOR for dependencies.
|
2018-06-20 17:05:41 +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-macs2
|
|
|
|
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 0.15.0 -> 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
|
|
|
|
rainbow
|
|
|
|
recombine
|
|
|
|
ruby-bio
|
|
|
|
rubygem-bio
|
|
|
|
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
|
biology/stacks: Enable OpenMP (oversight in previous commit)
|
2018-09-01 14:14:11 +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
|
|
|
|
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
|
|
|
|
tRNAscan-SE
|
Mark BROKEN: missing plist
|
2018-06-29 12:43:19 +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
|
|
|
|
Makefile
|
Remove expired ports:
|
2018-08-16 20:28:32 +00:00 |
