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freebsd-ports/biology
History
Danilo Egea Gondolfo f74ddaa6d0 - Swap back from net/openmpi3 to net/openmpi
2020-04-21 21:51:56 +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
Update devel/tbb to 2020.2 and bump dependent port's revisions
2020-04-01 14:14:51 +00:00
bwa
…
canu
biology/canu: Upgrade to 2.0
2020-03-20 18:14:23 +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
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clustalw
…
consed
Deprecate ports broken for more than 6 months
2020-04-04 20:51:40 +00:00
cufflinks
biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89
2020-03-31 06:42:22 +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 0.9.31.2
2020-03-21 22:11:25 +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
biology/fastp: Upgrade to 0.20.1
2020-04-09 16:17:02 +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
gcta
biology/gcta: Genome-wide Complex Trait Analysis
2020-04-15 15:22:04 +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
- Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)
2020-04-19 09:49:02 +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 2.5.8
2020-03-28 12:27:11 +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
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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
kallisto: Patch for build with GCC
2020-04-01 23:35:38 +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
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libsbml
Clean up Makefile
2020-02-08 19:01:40 +00:00
linux-foldingathome
Update to 7.6.9
2020-04-19 10:09:56 +00:00
mafft
…
mapm3
…
migrate
…
minimap2
…
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
- Swap back from net/openmpi3 to net/openmpi
2020-04-21 21:47:57 +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 2.10.4 -> 2.10.5
2020-04-04 20:09:00 +00:00
p5-AcePerl
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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
Cosmetic change
2020-04-02 12:01:30 +00:00
p5-Bio-Das
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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
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
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
- Swap back from net/openmpi3 to net/openmpi
2020-04-21 21:51:56 +00:00
plinkseq
Deprecate ports broken for more than 6 months
2020-04-04 20:51:40 +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: Upgrade to 2.2.7.1
2020-04-14 12:13:55 +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
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py-pysam
biology/py-pysam: Update 0.15.3 -> 0.15.4
2020-01-23 02:53:09 +00:00
py-xenaPython
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pyfasta
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
python-nexus
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rainbow
Update WWW
2020-03-31 23:18:09 +00:00
recombine
Fix after gets(3) retirement using gets_s(3).
2019-09-02 05:00:43 +00:00
ruby-bio
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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 5.0=>5.0.2
2020-03-22 16:54:04 +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
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seqtk
…
seqtools
Deprecate ports broken for more than 6 months
2020-04-04 20:51:40 +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 2.7.3a
2020-04-09 12:43:03 +00:00
stringtie
biology/stringtie: fix build on GCC architectures
2020-02-23 10:52:44 +00:00
t_coffee
Deprecate ports broken for more than 6 months
2020-04-04 20:51:40 +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
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
Deprecate ports broken for more than 6 months
2020-04-04 20:51:40 +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
biology/gcta: Genome-wide Complex Trait Analysis
2020-04-15 15:22:04 +00:00