..
artemis
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
Fix build on gcc-based archs by updating USES.
2018-09-22 05:30:31 +00:00
biococoa
Update Objective-C LLVM version to 6.0.
2018-09-26 15:23:37 +00:00
bowtie
Add DOCS options to ports that should have one.
2018-09-10 13:14:50 +00:00
bowtie2
Update devel/tbb to version 2019 and bump dependent port's revisions
2018-10-04 10:03:59 +00:00
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
Allow building on powerpc64.
2018-09-27 23:02:56 +00:00
iolib
- Update to 1-14-10
2018-09-28 18:47:49 +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
biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06
2018-10-07 18:29:16 +00:00
ngs-sdk
biology/ngs-sdk: Update 2.9.1 -> 2.9.2
2018-09-19 18:09:37 +00:00
njplot
p5-AcePerl
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
2018-10-06 13:06:42 +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
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
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
2018-07-29 22:18:44 +00:00
py-biom-format
biology/py-biom-format: Update to version 2.1.7
2018-10-06 15:28:01 +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
py-loompy
New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data
2018-09-21 08:04:50 +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
pyfasta
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
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
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
- Unbreak by adding missing pkg-plist
2018-09-28 00:12:48 +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
vcftools
biology/vcftools: Update to 0.1.16, a security release
2018-08-04 01:29:29 +00:00
velvet
wise
xmolwt
Makefile
biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/
2018-10-07 00:19:22 +00:00