freebsd-ports/biology
Yuri Victorovich 49bf1df227 biology/hhsuite: Update 3.2.0 -> 3.3.0
Reported by:	portscout
2020-08-27 04:28:24 +00:00
..
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/bcftools: Upgrade to 1.10.2 2020-08-03 18:16:54 +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 2.0.2 2020-08-07 11:20:11 +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 biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed 2020-08-14 04:59:29 +00:00
grappa
groopm biology/groopm: Remove python's 2.7 restriction placed here by mistake 2020-08-13 19:19:23 +00:00
haplohseq
hhsuite biology/hhsuite: Update 3.2.0 -> 3.3.0 2020-08-27 04:28:24 +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 2.5.17 2020-08-20 16:15:22 +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 biology/paml: fix the build with LLVM 11 2020-08-20 17:07:03 +00:00
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-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 biology/py-gtfparse: Update 1.2.0 -> 1.2.1 2020-08-07 04:13:00 +00:00
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 devel/ipython: Update to 7.17.0 2020-08-15 12:50:57 +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/samtools: Upgrade to 1.10 2020-08-03 18:22:06 +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 biology/vt: Patch to work with htslib 1.10.2 2020-08-03 17:42:32 +00:00
wise
Makefile Remove deprecated ports: 2020-08-15 10:50:58 +00:00