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freebsd-ports/biology
History
Yuri Victorovich 74ca3eaba7 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
..
abyss
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +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
biology/bcftools: update to 1.9
2018-08-02 19:30:57 +00:00
bedtools
biology/bedtools: unbreak with libc++ 8
2019-03-04 06:55:08 +00:00
biococoa
Move Objective-C ports to the v2 GNUstep ABI.
2019-02-03 15:37:58 +00:00
bowtie
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
bowtie2
Mark as broken on aarch64:
2019-03-29 22:13:11 +00:00
bwa
Multiple ports:
2018-01-31 01:07:07 +00:00
canu
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
cd-hit
biology/cd-hit: Upgrade to 4.8.1
2019-03-14 23:59:47 +00:00
cdbfasta
Multiple ports:
2018-01-31 01:07:07 +00:00
checkm
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
chemeq
…
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
…
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
2018-12-12 01:35:33 +00:00
diamond
biology/diamond: Update to version 0.9.24
2018-12-31 19:00:00 +00:00
dsr-pdb
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
emboss
…
exonerate
New port: biology/exonerate: Generic tool for sequence alignment
2018-07-13 07:02:16 +00:00
fasta
…
fasta3
…
fastahack
biology/fastahack: Utility for indexing and sequence extraction from FASTA files
2018-04-16 14:50:46 +00:00
fastdnaml
…
fastool
Multiple ports:
2018-01-31 01:07:07 +00:00
fastqc
[new port] biology/fastqc: Quality control tool for high throughput sequence data
2017-11-30 22:54:29 +00:00
fasttree
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
2018-12-12 01:35:33 +00:00
garlic
Return maho@'s ports to the pool after his commit bit expired.
2018-03-11 11:20:43 +00:00
gatk
devel/gradle: Update to 5.0
2018-12-04 17:53:46 +00:00
gff2ps
biology/gff2ps: update 0.98d to 0.98l
2018-12-19 17:34:29 +00:00
gmap
Multiple ports:
2018-01-31 01:07:07 +00:00
gperiodic
…
graphlan
New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees
2019-02-03 20:13:26 +00:00
grappa
…
groopm
biology/groopm fails to build with python3
2019-01-07 09:44:42 +00:00
hisat2
New port: biology/hisat2: Program for mapping next-generation sequencing reads
2019-01-11 16:02:05 +00:00
hmmer
vec_splats function is not supported by base GCC. Add USES=compiler:c11
2019-02-18 01:30:24 +00:00
htslib
biology/htslib: update to 1.9
2018-08-02 19:27:13 +00:00
hyphy
Change cmake default behaviour to outsource.
2018-12-25 20:25:39 +00:00
igv
biology/igv: Update 2.4.19 -> 2.5.0
2019-04-04 04:49:41 +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 1.6.10
2019-02-21 14:33:43 +00:00
jalview
…
jellyfish
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
kallisto
kallisto: Upgrade to 0.45.1, unbundle hstlib
2019-02-24 20:32:19 +00:00
lagan
…
lamarc
biology/lamarc: Fix build with Clang 6
2018-08-25 03:13:37 +00:00
libgtextutils
biology/libgtextutils: Unbreak for FreeBSD 12
2018-03-29 15:41:07 +00:00
libsbml
Change cmake default behaviour to outsource.
2018-12-25 20:25:39 +00:00
linux-foldingathome
biology/linux-foldingathome: reset maintainer by request
2018-07-27 02:19:43 +00:00
mafft
…
mapm3
…
migrate
Mark broken on armvX and mips.
2018-03-18 13:48:07 +00:00
molden
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
mopac
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +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
2018-12-12 01:35:33 +00:00
muscle
…
ncbi-blast+
Update dns/libidn2 to 2.1.1
2019-02-09 23:25:36 +00:00
ncbi-cxx-toolkit
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
ncbi-toolkit
Update dns/libidn2 to 2.1.1
2019-02-09 23:25:36 +00:00
ngs-sdk
biology/ngs-sdk: Update 2.9.4 -> 2.9.6
2019-03-31 03:31:59 +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
Use real PORTVERSION of devel/p5-Parse-RecDescent
2019-04-06 14:43:14 +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 1.007005 (1.7.5)
2019-02-22 19:54:12 +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
2018-12-12 01:35:33 +00:00
p5-TrimGalore
biology/p5-TrimGalore: Upgrade to 0.6.1
2019-03-24 21:44:17 +00:00
paml
biology/paml: Update to version 4.9i
2019-02-26 15:12:42 +00:00
pbbam
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
pbcopper
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +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
Add DOCS options to ports that should have one.
2018-09-10 13:14:50 +00:00
phylip
- Update to 3.697
2018-01-01 08:40:22 +00:00
phyml
Change 4 ports from net/mpich2 to net/mpich
2018-09-22 18:00:24 +00:00
plinkseq
Multiple ports:
2018-01-31 01:07:07 +00:00
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
New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities
2019-02-03 18:49:23 +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
2018-12-12 01:35:33 +00:00
py-biom-format
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-biopython
- Update to 1.73
2018-12-22 04:54:51 +00:00
py-bx-python
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-cutadapt
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-dnaio
biology/py-dnaio: Read and write FASTQ and FASTA
2019-03-24 19:40:26 +00:00
py-fastTSNE
biology/py-fastTSNE: Add the PORTSCOUT line
2019-03-31 16:57:54 +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
2018-12-12 01:35:33 +00:00
py-loompy
biology/py-loompy: Update 2.0.16 -> 2.0.17
2019-02-02 21:38:48 +00:00
py-macs2
Bump PORTREVISION for ports depending on the canonical version of GCC
2018-12-12 01:35:33 +00:00
py-orange3-bioinformatics
Fix Qt5 symbol version scripts to put the catch-all clause first. When
2019-01-16 11:13:44 +00:00
py-orange3-single-cell
Fix Qt5 symbol version scripts to put the catch-all clause first. When
2019-01-16 11:13:44 +00:00
py-pyfaidx
Bump a few PORTREVISIONs after r498529
2019-04-10 06:18:31 +00:00
py-pysam
biology/py-pysam: Update 0.15.1 -> 0.15.2
2019-01-26 04:15:54 +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
2018-12-12 01:35:33 +00:00
pyfasta
- Update WWW
2019-02-07 09:30:40 +00:00
python-nexus
- Update to 1.63
2018-09-22 08:54:58 +00:00
rainbow
biology/rainbow: Efficient clustering and assembling of short reads
2018-04-02 16:50:46 +00:00
recombine
…
ruby-bio
…
rubygem-bio
Update to 1.5.2
2018-09-21 18:08:24 +00:00
samtools
biology/samtools: update to 1.9
2018-08-02 19:28:36 +00:00
seaview
biology/seaview: Fix build with Clang 6
2018-09-08 09:01:35 +00:00
seqan
biology/seqan-apps, biology/seqan: Update to 2.4.0
2018-03-10 06:21:37 +00:00
seqan1
…
seqan-apps
devel/boost-*: update to 1.70.0
2019-04-12 06:36:31 +00:00
seqio
- Switch to options helpers
2017-11-26 09:00:21 +00:00
seqtk
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format
2018-04-03 20:57:05 +00:00
seqtools
biology/seqtools: fix build on current, if lld is lld7
2019-01-07 19:54:40 +00:00
sim4
…
slclust
Multiple ports:
2018-01-31 01:07:07 +00:00
smithwaterman
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
2018-04-15 17:45:52 +00:00
stacks
biology/stacks: Upgrade to 2.3
2019-01-12 15:53:00 +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
2018-12-12 01:35:33 +00:00
tabixpp
biology/tabixpp: C++ wrapper to tabix indexer
2018-04-14 23:52:16 +00:00
treepuzzle
…
trimadap
Mark as broken on aarch64, and, where appropriate, armvX.
2018-06-21 23:52:37 +00:00
trimmomatic
Multiple ports:
2018-01-31 01:07:07 +00:00
tRNAscan-SE
- Unbreak by adding missing pkg-plist
2018-09-28 00:12:48 +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 1.70.0
2019-04-12 06:36:31 +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
- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
2018-01-11 18:09:00 +00:00
wise
…
Makefile
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