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freebsd-ports/biology
History
Jason W. Bacon e4868fdb92 biology/canu: Upgrade to 1.9 
Numerous bug fixes and enhancements

Reported by:    portscout
2019-11-08 14:03:15 +00:00
..
abyss
devel/openmp: update to 9.0.0
2019-09-21 18:59:57 +00:00
artemis
…
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
…
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 0.9.28
2019-11-07 14:12:07 +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
…
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
biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43
2019-07-26 18:03:08 +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: 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
…
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
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-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
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +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
…
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: update to 3.3.20190909
2019-09-10 21:04:16 +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
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
…
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
Add USES=xorg USES=gl, ports categories b
2019-11-04 21:08:20 +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
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
…
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
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
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +00:00
unanimity
Mark a few ports BROKEN, unfetchable
2019-11-06 12:48:32 +00:00
vcflib
…
vcftools
…
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
Remove expired ports:
2019-10-16 15:29:32 +00:00