..
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
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
bedtools
bioawk
biology/bioawk: BWK awk modified for biological data
2020-06-05 02:45:33 +00:00
biococoa
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 2020.3 and bump dependent ports' revisions
2020-07-17 10:12:25 +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/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
cytoscape
ddocent
diamond
biology/diamond: Update to version 2.0.0
2020-07-28 02:39:00 +00:00
dsr-pdb
emboss
- update libgd to 2.3.0
2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
biology/gatk: Update 4.1.7.0 -> 4.1.8.0
2020-07-09 00:40:56 +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
graphlan
grappa
groopm
haplohseq
hhsuite
biology/hhsuite: fix build on powerpc64 elfv2
2020-05-11 19:33:32 +00:00
hisat2
hmmer
htslib
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
hyphy
biology/hyphy: Update to version 2.5.15
2020-06-28 16:40:33 +00:00
igv
infernal
iolib
iqtree
biology/iqtree: Update to version 2.0.6
2020-05-30 18:43:26 +00:00
jalview
jellyfish
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
kallisto
biology/kallisto: Revert to 0.46.1
2020-08-03 15:45:21 +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
mummer
muscle
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
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
p5-Bio-FeatureIO
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-Bio-Variation
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
p5-transdecoder
p5-TrimGalore
paml
pbbam
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
pbcopper
Deprecate ports broken for more than 6 months
2020-07-26 07:32:00 +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
biology/phyml: update to 3.3.20200621
2020-07-10 09:45:48 +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
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
py-Genesis-PyAPI
py-gffutils
Unbreak bulk -a
2020-07-14 07:59:28 +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
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
recombine
ruby-bio
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
2020-05-05 14:22:09 +00:00
rubygem-bio
Update to 2.0.1
2020-07-24 07:49:43 +00:00
rubygem-bio-executables
Add rubygem-bio-executables 1.0.0
2020-07-24 07:08:00 +00:00
rubygem-bio-old-biofetch-emulator
Add rubygem-bio-old-biofetch-emulator 1.0.0
2020-07-24 07:08:05 +00:00
rubygem-bio-shell
Add rubygem-bio-shell 1.0.0
2020-07-24 07:08:11 +00:00
samtools
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
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
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star
stringtie
subread
biology/subread: Read alignment, quantification and mutation discovery
2020-06-05 01:55:49 +00:00
tabixpp
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
biology/ugene: prepare for Qt5-5.15
2020-05-19 18:00:02 +00:00
vcflib
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
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
Add rubygem-bio-shell 1.0.0
2020-07-24 07:08:11 +00:00
fb3f006dcf