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Sunpoet Po-Chuan Hsieh 2b9ee80386 Add p5-Bio-DB-NCBIHelper 1.7.6 
Bio::DB::NCBIHelper provides a single place to setup some common methods for
querying NCBI web databases. This module just centralizes the methods for
constructing a URL for querying NCBI GenBank and NCBI GenPept and the common
HTML stripping done in postprocess_data().

WWW: https://metacpan.org/release/Bio-DB-NCBIHelper
2019-12-08 16:49:25 +00:00
..
abyss devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
artemis Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
avida biology/avida: unbreak on powerpc64 2019-10-23 16:25:10 +00:00
babel
bamtools Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
bcftools math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
bedtools biology/bedtools: Upgrade to 2.29.0 2019-09-13 13:21:59 +00:00
biococoa Move Objective-C ports to the v2 GNUstep ABI. 2019-02-03 15:37:58 +00:00
bolt-lmm devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
bowtie2 Update devel/tbb to 2019.8 and bump dependent ports' revisions 2019-09-25 10:03:49 +00:00
bwa
canu biology/canu: Upgrade to 1.9 2019-11-08 14:03:15 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
cdbfasta
checkm biology/checkm: Update 1.0.17 -> 1.0.18 2019-08-19 08:25:29 +00:00
clustal-omega
clustalw
consed Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
cufflinks devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
cytoscape Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
ddocent Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
diamond biology/diamond: Update to v0.9.29 2019-11-20 17:14:29 +00:00
dsr-pdb devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
emboss Sprinkle more USES=xorg 2019-11-07 20:19:59 +00:00
exonerate New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00
fasta Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
fasta3 Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
fastahack biology/fastahack: Upgrade to 1.0.0 2019-10-06 21:34:32 +00:00
fastdnaml
fastool
fastp Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
fastqc biology/fastqc: Upgrade to 0.11.8 2019-09-21 02:44:54 +00:00
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
fastx-toolkit
figtree New port: biology/figtree: Graphical viewer of phylogenetic trees 2019-02-03 21:14:38 +00:00
fluctuate
freebayes Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
garlic Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
gatk Create devel/gradle5 in preparation of devel/gradle update 2019-11-20 09:51:43 +00:00
gemma math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
gff2ps biology/gff2ps: update 0.98d to 0.98l 2018-12-19 17:34:29 +00:00
gmap Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
gperiodic a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
graphlan New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees 2019-02-03 20:13:26 +00:00
grappa
groopm Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
haplohseq biology/haplohseq: Switch to distfile with example data 2019-11-17 15:00:13 +00:00
hhsuite devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
hisat2 New port: biology/hisat2: Program for mapping next-generation sequencing reads 2019-01-11 16:02:05 +00:00
hmmer Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
htslib biology/htslib: update to 1.9 2018-08-02 19:27:13 +00:00
hyphy Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
igv biology/igv: Update 2.5.2 -> 2.5.3 2019-06-01 20:49:20 +00:00
infernal Allow building on powerpc64. 2018-09-27 23:02:56 +00:00
iolib - Fix build in head i386 2019-04-01 19:33:15 +00:00
iqtree biology/iqtree: Update to version 1.6.12 2019-08-27 01:19:11 +00:00
jalview Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
jellyfish Drop C++11 workaround for GCC < 6 after r449590 2019-09-14 22:01:13 +00:00
kallisto biology/kallisto: Upgrade to 0.46.1 2019-11-06 00:18:14 +00:00
lagan Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libbigwig New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00
libgtextutils
libsbml Use USES=pathfix 2019-06-22 21:48:14 +00:00
mafft
mapm3
migrate
minimap2 biology/minimap2: Upgrade to 2.17 2019-05-05 14:56:07 +00:00
molden Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mothur biology/mothur: Update 1.42.3 -> 1.43.0 2019-10-05 17:04:42 +00:00
mrbayes Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
mummer Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
ncbi-cxx-toolkit Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
ncbi-toolkit biologi/ncbi-toolkit: Remove dependency on libXp 2019-09-28 10:52:57 +00:00
ngs-sdk biology/ngs-sdk: Update 2.9.6 -> 2.10.0 2019-08-31 15:09:47 +00:00
p5-AcePerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene Update to 1.73 2018-10-10 10:23:10 +00:00
p5-Bio-Cluster Add p5-Bio-Cluster 1.7.3 2019-02-20 20:46:37 +00:00
p5-Bio-Coordinate Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das-Lite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-DB-EMBL Add p5-Bio-DB-EMBL 1.7.4 2019-12-08 16:49:19 +00:00
p5-Bio-DB-NCBIHelper Add p5-Bio-DB-NCBIHelper 1.7.6 2019-12-08 16:49:25 +00:00
p5-Bio-FeatureIO Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-GFF3 Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Glite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Graphics Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-MAGETAB Fix typo 2019-04-23 14:11:50 +00:00
p5-Bio-NEXUS Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Phylo Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-SCF - Add LICENSE 2019-03-30 09:01:08 +00:00
p5-BioPerl Update to 1.007006 (1.7.6) 2019-09-07 22:44:02 +00:00
p5-BioPerl-Run Update to 1.007003 2019-02-20 20:46:58 +00:00
p5-transdecoder Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
p5-TrimGalore biology/p5-TrimGalore: Upgrade to 0.6.5 2019-11-26 16:20:12 +00:00
paml biology/paml: Update to version 4.9j 2019-11-22 15:32:40 +00:00
pbbam biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pbcopper biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pbseqan biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pear-merger
phrap Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phred Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
phylip Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
phyml biology/phyml: disable -march=native 2019-12-06 13:04:41 +00:00
plinkseq Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
primer3 biology/primer3: Fix build with Clang 6 2018-08-25 03:35:46 +00:00
prodigal biology/prodigal: Eliminate a very old version from the portscout discovery process 2019-10-12 15:40:21 +00:00
prodigy-lig Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
protomol Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-biom-format - Limit python version (does not build with 3.7+) 2019-11-08 12:12:42 +00:00
py-biopython Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-bx-python biology/py-bx-python: Update 0.8.4 -> 0.8.6 2019-11-23 05:53:50 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.7 2019-11-23 14:45:53 +00:00
py-dnaio biology/py-dnaio: Upgrade to 0.4.1 2019-11-23 14:40:00 +00:00
py-fastTSNE devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
py-Genesis-PyAPI
py-gffutils Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
py-gtfparse Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-loompy Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-macs2 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-multiqc biology/py-multiqc: Upgrade to 1.8 2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-orange3-single-cell Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-pyfaidx Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
py-pysam biology/py-pysam: Update 0.15.2 -> 0.15.3 2019-08-31 15:49:18 +00:00
py-xenaPython New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub 2019-04-12 17:01:10 +00:00
pycogent Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
pyfasta Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
python-nexus - Update to 1.63 2018-09-22 08:54:58 +00:00
rainbow
recombine Fix after gets(3) retirement using gets_s(3). 2019-09-02 05:00:43 +00:00
ruby-bio
rubygem-bio Update to 1.5.2 2018-09-21 18:08:24 +00:00
samtools Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
seaview Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
seqan
seqan-apps devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqio
seqtk
seqtools Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
sim4
slclust
smithwaterman
stacks Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
star biology/star: Upgrade to 2.7.2d 2019-10-06 22:18:31 +00:00
stringtie New port: biology/stringtie: Transcript assembly and quantification for RNA-seq 2018-07-11 21:32:39 +00:00
t_coffee Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
tabixpp
tophat biology/tophat: Fast splice junction mapper for RNA-Seq reads 2019-09-27 00:49:48 +00:00
treekin Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
treepuzzle
trimadap biology/trimadap: Mark only for amd64 and i386 2019-05-11 00:18:24 +00:00
trimmomatic Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.3 2019-06-08 01:31:18 +00:00
ugene Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
unanimity biology/unanimity: Remove erroneous BROKEN 2019-11-28 05:46:04 +00:00
vcflib
vcftools biology/vcftools: Update to 0.1.16, a security release 2018-08-04 01:29:29 +00:00
velvet
viennarna Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
vsearch biology/vsearch: Update to 2.13.4 2019-05-11 13:42:33 +00:00
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile Add p5-Bio-DB-NCBIHelper 1.7.6 2019-12-08 16:49:25 +00:00