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1af7d786f7
freebsd-ports/biology
History
Tobias Kortkamp 7a80d0bf6c Deprecate java/openjfx8-devel consumers 
Chase r527795 and put a deprecation notice on all openjfx8-devel
dependent ports too.

Also deprecate devel/gradle4 which is only needed to build igv and
openjfx8-devel.
2020-03-19 09:33:13 +00:00
..
abyss Drop dependency on devel/openmp 2020-03-08 21:56:36 +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 devel/jsoncpp: Update 1.8.1 -> 1.9.2 2020-01-13 21:38:35 +00:00
bcftools math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
bedtools biology/bedtools: Upgrade to 2.29.2 2019-12-19 01:04:11 +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 Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
bowtie2 biology/bowtie2: Upgrade to 2.4.1 2020-03-01 16:01:12 +00:00
bwa
canu devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +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 1.72.0 2019-12-11 17:53:48 +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 version 0.9.30 2020-02-03 15:55:05 +00:00
dsr-pdb devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
emboss Sprinkle more USES=xorg 2019-11-07 20:19:59 +00:00
exonerate
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
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 biology/gatk: Update 4.1.4.1 -> 4.1.5.0 2020-03-04 08:47:55 +00:00
gemma Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
gff2ps
gmap Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
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 Drop dependency on devel/openmp 2020-03-08 21:56:36 +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 2.5.6 2020-03-17 18:17:16 +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 - 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 biology/jellyfish: Patch for clang 10 2020-03-07 19:25:54 +00:00
kallisto biology/kallisto: Upgrade to 0.46.2 2020-02-15 23:09:19 +00:00
lagan Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
lamarc
libbigwig New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00
libgtextutils
libsbml Clean up Makefile 2020-02-08 19:01:40 +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 biology/mrbayes: Update to version 3.2.7 2020-02-29 23:24:39 +00:00
mummer Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
muscle biology/muscle: unbreak in -CURRENT 2020-01-17 16:49:03 +00:00
ncbi-blast+ biology/ncbi-blast+: Upgrade to 2.10.0 2019-12-26 16:21:17 +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 2.10.2 -> 2.10.4 2020-03-07 19:58:39 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene Update *_DEPENDS 2020-01-08 18:36:30 +00:00
p5-Bio-Cluster Update *_DEPENDS 2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
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
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB Fix typo 2019-04-23 14:11:50 +00:00
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF - Add LICENSE 2019-03-30 09:01:08 +00:00
p5-Bio-Variation Update to 1.7.5 2020-01-08 18:36:35 +00:00
p5-BioPerl Update to 1.007007 (1.7.7) 2019-12-08 16:57:23 +00:00
p5-BioPerl-Run Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago 2020-01-08 18:36:40 +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 devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
pbcopper Mark BROKEN: fails to build 2020-03-10 14:17:19 +00:00
pbseqan biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pear-merger
phrap
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
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 Deprecate a few ports 2020-02-23 15:25:53 +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 biology/py-bx-python: Update 0.8.6 -> 0.8.8 2020-02-15 20:08:30 +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 Drop dependency on devel/openmp 2020-03-08 21:56:36 +00:00
py-Genesis-PyAPI
py-gffutils biology/py-gffutils: Update 0.9 -> 0.10 2019-12-31 05:16:09 +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 biology/py-macs2: Bump revision for previous run dep addition 2020-02-09 14:23:43 +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 0.15.3 -> 0.15.4 2020-01-23 02:53:09 +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
pyfasta Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
python-nexus
rainbow
recombine Fix after gets(3) retirement using gets_s(3). 2019-09-02 05:00:43 +00:00
ruby-bio
rubygem-bio
samtools Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
seaview biology/seaview: Update version 4.7=>5.0 2020-02-05 18:35:42 +00:00
seqan
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqan-apps devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +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 biology/stringtie: fix build on GCC architectures 2020-02-23 10:52:44 +00:00
t_coffee Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +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 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 2.0.5 2020-01-13 17:36:57 +00:00
ugene Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
vcflib
vcftools
velvet
viennarna biology/viennarna: Update 2.4.13 -> 2.4.14 2020-01-06 04:17:48 +00:00
vsearch biology/vsearch: Upgrade to 2.14.2 2020-02-19 22:34:36 +00:00
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile Remove expired ports: 2020-01-27 15:34:18 +00:00