..
abyss
Chanse update of devel/libffi
2020-07-04 18:11:42 +00:00
artemis
avida
babel
bamtools
Bump devel/jsoncpp consumers after r540853.
2020-06-30 17:46:18 +00:00
bcftools
bedtools
biology/bedtools: Upgrade to 2.29.2
2019-12-19 01:04:11 +00:00
bioawk
biology/bioawk: BWK awk modified for biological data
2020-06-05 02:45:33 +00:00
biococoa
Return theraven's ports to the pool after safekeeping his commit bit.
2020-03-05 20:49:05 +00:00
bolt-lmm
Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
2020-05-06 16:11:14 +00:00
bowtie
biology/bowtie: Unbreak build with GCC 10
2020-07-04 10:46:08 +00:00
bowtie2
Update devel/tbb to 2020.2 and bump dependent port's revisions
2020-04-01 14:14:51 +00:00
bwa
canu
Mark as BROKEN on powerpc64:
2020-05-17 02:25:16 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89
2020-03-31 06:42:22 +00:00
cytoscape
ddocent
diamond
biology/diamond: Update to version 0.9.36
2020-07-03 11:22:49 +00:00
dsr-pdb
devel/boost-*: update to 1.72.0
2019-12-11 17:53:48 +00:00
emboss
- update libgd to 2.3.0
2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
biology/fastp: Upgrade to 0.20.1
2020-04-09 16:17:02 +00:00
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
biology/gatk: Update 4.1.5.0 -> 4.1.7.0
2020-05-28 02:26:51 +00:00
gcta
Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
2020-05-06 16:11:14 +00:00
gemma
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
2020-05-06 16:39:12 +00:00
gff2ps
gmap
gperiodic
- Update WWW
2020-01-19 09:30:22 +00:00
graphlan
Deprecate a few ports
2020-02-23 15:25:53 +00:00
grappa
groopm
Deprecate a few ports
2020-02-23 15:25:53 +00:00
haplohseq
Deprecate some ports using deprecated version of python
2020-03-08 17:01:46 +00:00
hhsuite
biology/hhsuite: fix build on powerpc64 elfv2
2020-05-11 19:33:32 +00:00
hisat2
hmmer
biology/hmmer: update to 3.3
2020-01-29 05:55:12 +00:00
htslib
hyphy
biology/hyphy: Update to version 2.5.15
2020-06-28 16:40:33 +00:00
igv
Deprecate java/openjfx8-devel consumers
2020-03-19 09:33:13 +00:00
infernal
biology/infernal: update to 1.1.3
2020-01-27 17:57:14 +00:00
iolib
iqtree
biology/iqtree: Update to version 2.0.6
2020-05-30 18:43:26 +00:00
jalview
jellyfish
biology/jellyfish: Patch for clang 10
2020-03-07 19:25:54 +00:00
kallisto
kallisto: Patch for build with GCC
2020-04-01 23:35:38 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml
Move devel/swig30 to devel/swig and update to 4.0.1
2020-06-17 18:17:45 +00:00
linux-foldingathome
Update to 7.6.13
2020-05-09 13:21:29 +00:00
mafft
mapm3
migrate
minimap2
molden
mopac
mothur
Update devel/gmake to 4.3.
2020-05-09 19:24:49 +00:00
mrbayes
- Swap back from net/openmpi3 to net/openmpi
2020-04-21 21:47:57 +00:00
mummer
muscle
biology/muscle: unbreak in -CURRENT
2020-01-17 16:49:03 +00:00
ncbi-blast+
Bump PORTREVISION for security/nettle shlib change
2020-05-16 10:51:32 +00:00
ncbi-cxx-toolkit
ncbi-toolkit
Bump PORTREVISION for security/nettle shlib change
2020-05-16 10:51:32 +00:00
ngs-sdk
biology/ngs-sdk: Update 2.10.4 -> 2.10.5
2020-04-04 20:09:00 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
Update *_DEPENDS
2020-01-08 18:36:30 +00:00
p5-Bio-Cluster
Update *_DEPENDS
2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate
Cosmetic change
2020-04-02 12:01:30 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
Add p5-Bio-DB-NCBIHelper 1.7.6
2019-12-08 16:49:25 +00:00
p5-Bio-FeatureIO
Cosmetic change
2020-04-02 12:01:35 +00:00
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation
Update to 1.7.5
2020-01-08 18:36:35 +00:00
p5-BioPerl
Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
2020-06-26 11:55:23 +00:00
p5-BioPerl-Run
Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago
2020-01-08 18:36:40 +00:00
p5-transdecoder
p5-TrimGalore
paml
pbbam
devel/boost-*: update to 1.72.0
2019-12-11 17:53:48 +00:00
pbcopper
Mark BROKEN: fails to build
2020-03-10 14:17:19 +00:00
pbseqan
pear-merger
phrap
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
2020-05-27 11:59:13 +00:00
phred
phylip
phyml
- Swap back from net/openmpi3 to net/openmpi
2020-04-21 21:51:56 +00:00
picard-tools
biology/picard-tools: CLI tools for manipulating sequencing data
2020-06-13 13:54:47 +00:00
plink
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
2020-05-06 16:39:12 +00:00
primer3
prodigal
prodigy-lig
Unbreak bulk -a
2020-06-13 15:05:44 +00:00
protomol
psi88
biology/psi88: Unbreak build with GCC 10
2020-07-04 12:15:58 +00:00
py-biom-format
Deprecate a few ports
2020-02-23 15:25:53 +00:00
py-biopython
biology/py-biopython: Set python requirement to 3.6+
2020-06-13 13:42:12 +00:00
py-bx-python
biology/py-bx-python: Update 0.8.8 -> 0.8.9
2020-06-26 04:17:11 +00:00
py-cutadapt
py-dnaio
biology/py-dnaio: Upgrade to 0.4.2
2020-05-24 15:23:15 +00:00
py-ete3
New port: biology/py-ete3: Framework for the analysis and visualization of trees
2020-05-16 00:13:09 +00:00
py-fastTSNE
Drop dependency on devel/openmp
2020-03-08 21:56:36 +00:00
py-Genesis-PyAPI
py-gffutils
biology/py-gffutils: Update 0.10 -> 0.10.1
2020-06-16 02:10:08 +00:00
py-gtfparse
py-hits
New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
2020-05-16 03:11:05 +00:00
py-loompy
biology/py-loompy: Update 2.0.17 -> 3.0.6
2020-06-16 02:26:08 +00:00
py-macs2
biology/py-macs2: Upgrade to 2.2.7.1
2020-04-14 12:13:55 +00:00
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
Update Sphinx
2020-05-11 23:51:58 +00:00
py-pandas-charm
Clean up some things
2020-05-30 00:57:02 +00:00
py-pyfaidx
py-pysam
biology/py-pysam: Update 0.15.4 -> 0.16.0
2020-06-09 05:03:48 +00:00
py-scikit-bio
biology/py-scikit-bio: Fix license
2020-05-16 02:29:20 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow
Update WWW
2020-03-31 23:18:09 +00:00
recombine
ruby-bio
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
2020-05-05 14:22:09 +00:00
rubygem-bio
samtools
scrm
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
2020-05-15 07:30:34 +00:00
seaview
biology/seaview: Update version 5.0.3=>5.0.4
2020-06-22 17:34:44 +00:00
seqan
seqan1
seqan-apps
devel/boost-*: update to 1.72.0
2019-12-11 17:53:48 +00:00
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star
biology/star: Upgrade to 2.7.3a
2020-04-09 12:43:03 +00:00
stringtie
biology/stringtie: fix build on GCC architectures
2020-02-23 10:52:44 +00:00
subread
biology/subread: Read alignment, quantification and mutation discovery
2020-06-05 01:55:49 +00:00
tabixpp
tophat
Deprecate some ports using deprecated version of python
2020-03-08 17:01:46 +00:00
treekin
Fix math/openblas and bump dependent ports
2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
biology/tRNAscan-SE: update to 2.0.5
2020-01-13 17:36:57 +00:00
ugene
biology/ugene: prepare for Qt5-5.15
2020-05-19 18:00:02 +00:00
vcflib
vcftools
velvet
viennarna
- update libgd to 2.3.0
2020-05-04 21:31:39 +00:00
vsearch
biology/vsearch: Update to 2.15.0
2020-06-20 14:31:59 +00:00
vt
Add compiler:c++0x to USES to fix build on GCC-based systems:
2020-06-05 03:49:53 +00:00
wise
Makefile
biology/picard-tools: CLI tools for manipulating sequencing data
2020-06-13 13:54:47 +00:00
0e32330f15