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mirror of https://git.FreeBSD.org/ports.git synced 2024-12-22 04:17:44 +00:00
freebsd-ports/biology
2020-06-04 18:28:13 +00:00
..
abyss biology/abyss: Update 2.2.3 -> 2.2.4 2020-05-30 09:10:44 +00:00
artemis
avida
babel
bamtools devel/jsoncpp: Update 1.8.1 -> 1.9.2 2020-01-13 21:38:35 +00:00
bcftools
bedtools
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
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 0.9.33 2020-06-03 21:44:36 +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 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 2.5.14 2020-05-30 19:39:11 +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 Clean up Makefile 2020-02-08 19:01:40 +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
p5-Bio-Cluster
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
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
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
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
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
protomol
psi88
py-biom-format Deprecate a few ports 2020-02-23 15:25:53 +00:00
py-biopython biology/py-biopython: Upgrade to 1.77 2020-05-29 02:03:29 +00:00
py-bx-python biology/py-bx-python: Update 0.8.6 -> 0.8.8 2020-02-15 20:08:30 +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
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
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 0.15.3 -> 0.15.4 2020-01-23 02:53:09 +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=>5.0.2 2020-03-22 16:54:04 +00:00
seqan
seqan1
seqan-apps
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
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: Upgrade to 2.14.2 2020-02-19 22:34:36 +00:00
vt bioloty/vt: Discovers short variants from Next Generation Sequencing data 2020-06-04 18:28:13 +00:00
wise
Makefile bioloty/vt: Discovers short variants from Next Generation Sequencing data 2020-06-04 18:28:13 +00:00