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freebsd-ports/biology
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Sunpoet Po-Chuan Hsieh 8ed0c4eaeb Add rubygem-bio-old-biofetch-emulator 1.0.0 
bio-old-biofetch-emulator emulates Bio::Fetch object in BioRuby as if
discontinued BioRuby BioFetch server were still alive. It overrides methods and
objects in Bio::Fetch, and if the old BioRuby BioFetch server's URL is given, it
intercepts all requests and converts them into existing web services such as
TogoWS, KEGG REST API, NCBI E-Utilities, and GenomeNet(genome.jp).

WWW: https://github.com/ngoto/bioruby-old-biofetch-emulator
2020-07-24 07:08:05 +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
bedtools
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 2020.3 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/cufflinks: fix build on GCC architectures 2020-07-08 10:37:07 +00:00
cytoscape
ddocent
diamond biology/diamond: Update to version 0.9.36 2020-07-03 11:22:49 +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 4.1.7.0 -> 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 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
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 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
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 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 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 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 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
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
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
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
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 Add rubygem-bio-old-biofetch-emulator 1.0.0 2020-07-24 07:08:05 +00:00