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2019Q4
freebsd-ports/biology
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Niclas Zeising dcb57b7643 biologi/ncbi-toolkit: Remove dependency on libXp 
Remove the dependency on libXp from ncbi-toolkit, since libXp is deprecated
and it isn't needed.
Remove deprecation from ncbi-toolkit.
2019-09-28 10:52:57 +00:00
..
abyss devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
artemis biology/artemis: Update 9 -> 17.0.1-11 2018-06-11 17:45:56 +00:00
avida Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
babel
bamtools Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
bcftools Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +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 devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +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
chemeq Deprecate a few ports 2019-09-15 17:28:08 +00:00
clustal-omega biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw 2018-05-21 22:15:26 +00:00
clustalw biology/clustalw: Fix license, take maintainership 2018-05-21 01:13:40 +00:00
consed Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
cufflinks devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +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 version 0.9.26 2019-09-18 18:45:09 +00:00
dsr-pdb devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
emboss Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +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
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 biology/fastx-toolkit: Fix build on FreeBSD 12 2018-05-16 15:13:43 +00:00
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
gatk biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43 2019-07-26 18:03:08 +00:00
gemma Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 biology/gperiodic: fix NLS and other rough edges 2019-08-23 15:26:55 +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: Identify regions of allelic imbalance 2019-09-16 01:07:31 +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
jellyfish Drop C++11 workaround for GCC < 6 after r449590 2019-09-14 22:01:13 +00:00
kallisto Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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
linux-foldingathome Deprecate a few ports 2019-09-15 17:28:08 +00:00
mafft
mapm3
migrate
minimap2 biology/minimap2: Upgrade to 2.17 2019-05-05 14:56:07 +00:00
molden Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mothur Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mrbayes Update devel/readline to 8.0 2019-04-09 14:04:49 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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-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 0.6.4 2019-09-21 02:51:26 +00:00
paml biology/paml: Update to version 4.9i 2019-02-26 15:12:42 +00:00
pbbam devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
pbcopper devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
pbseqan biology/pbseqan: Mark deprecated 2019-02-20 01:53:35 +00:00
pear-merger Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
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
phyml biology/phyml: update to 3.3.20190909 2019-09-10 21:04:16 +00:00
plinkseq
primer3 biology/primer3: Fix build with Clang 6 2018-08-25 03:35:46 +00:00
prodigal New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes 2019-02-03 18:08:14 +00:00
prodigy-lig Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
protomol biology/protomol: Fix doubled USES overwriting the old value 2018-08-25 03:47:25 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.5 2019-09-13 13:17:26 +00:00
py-dnaio biology/py-dnaio: Read and write FASTQ and FASTA 2019-03-24 19:40:26 +00:00
py-fastTSNE devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
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: Aggregate bioinformatics analysis reports 2019-09-23 16:09:30 +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 biology/seaview: Fix build with Clang 6 2018-09-08 09:01:35 +00:00
seqan
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqan-apps devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
seqio
seqtk
seqtools Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
stringtie New port: biology/stringtie: Transcript assembly and quantification for RNA-seq 2018-07-11 21:32:39 +00:00
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 biology/trimmomatic: Upgrade to 0.39 2019-09-14 14:45:49 +00:00
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.3 2019-06-08 01:31:18 +00:00
ugene Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
unanimity devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
vcflib Mark these ports as broken on aarch64. 2018-06-22 00:03:08 +00:00
vcftools biology/vcftools: Update to 0.1.16, a security release 2018-08-04 01:29:29 +00:00
velvet
viennarna Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
vsearch biology/vsearch: Update to 2.13.4 2019-05-11 13:42:33 +00:00
wise Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
Makefile biology/tophat: Fast splice junction mapper for RNA-Seq reads 2019-09-27 00:49:48 +00:00