| .. |
|
abyss
|
biology/abyss: fix build on big-endian architectures
|
2019-06-21 11:43:09 +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 |
|
bolt-lmm
|
biology/bolt-lmm: Mixed model association testing and variance component analysis
|
2019-05-26 03:36:49 +00:00 |
|
bowtie
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
bowtie2
|
biology/bowtie2: Clarify CPU-specificity
|
2019-04-24 17:41:27 +00:00 |
|
bwa
|
|
|
|
canu
|
biology/canu: Fix build on powerpc64 and aarch64
|
2019-04-18 12:15:56 +00:00 |
|
cd-hit
|
biology/cd-hit: Upgrade to 4.8.1
|
2019-03-14 23:59:47 +00:00 |
|
cdbfasta
|
|
|
|
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
|
|
|
|
cufflinks
|
biology/cufflinks: Fix build on i386 by removing the hard-coded -m64
|
2019-05-29 07:02:28 +00:00 |
|
cytoscape
|
biology/cytoscape: Fix license
|
2018-08-12 06:29:51 +00:00 |
|
ddocent
|
biology/ddocent: Upgrade to 2.7.8
|
2019-05-04 15:09:10 +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
|
|
|
|
fastp
|
biology/fastp: Remove redundant USE_GCC
|
2019-05-20 23:41:08 +00:00 |
|
fastqc
|
|
|
|
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 |
|
gemma
|
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC
|
2019-05-18 22:41:15 +00:00 |
|
gff2ps
|
biology/gff2ps: update 0.98d to 0.98l
|
2018-12-19 17:34:29 +00:00 |
|
gmap
|
Enable workaround for building on powerpc64.
|
2019-06-21 11:15:08 +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 |
|
hhsuite
|
biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist or isn't detected.
|
2019-05-22 02:50:56 +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 2.5.2 -> 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 1.6.10
|
2019-02-21 14:33:43 +00:00 |
|
jalview
|
|
|
|
jellyfish
|
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64
|
2019-05-13 16:23:35 +00:00 |
|
kallisto
|
biology/kallisto: Upgrade to 0.46.0
|
2019-06-12 15:24:55 +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
|
Use USES=pathfix
|
2019-06-22 21:48:14 +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 |
|
minimap2
|
biology/minimap2: Upgrade to 2.17
|
2019-05-05 14:56:07 +00:00 |
|
molden
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
mopac
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
mothur
|
biology/mothur: Update 1.42.1-3 -> 1.42.2
|
2019-06-19 23:54:44 +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+
|
biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl
|
2019-06-14 00:37:59 +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
|
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 1.007005 (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
|
|
|
|
phyml
|
- Update to 3.3.20190321
|
2019-05-20 09:17:29 +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
|
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
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +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
|
biology/py-bx-python: Update 0.8.2 -> 0.8.4
|
2019-06-19 08:08:31 +00:00 |
|
py-cutadapt
|
biology/py-cutadapt: Upgrade to 2.3
|
2019-04-27 01:26:17 +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: phase out
|
2019-05-08 16:05:53 +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 |
|
seqan-apps
|
devel/boost-*: update to 1.70.0
|
2019-04-12 06:36:31 +00:00 |
|
seqan1
|
|
|
|
seqio
|
|
|
|
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
|
|
|
|
smithwaterman
|
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm
|
2018-04-15 17:45:52 +00:00 |
|
stacks
|
biology/stacks: Remove obsolete pkg-message regarding web interface
|
2019-05-10 21:15:42 +00:00 |
|
star
|
biology/star: Force newer GCC on platforms with GCC 4.2 base
|
2019-05-02 00:39:51 +00:00 |
|
stringtie
|
New port: biology/stringtie: Transcript assembly and quantification for RNA-seq
|
2018-07-11 21:32:39 +00:00 |
|
t_coffee
|
Related to revision 499061 bump ports with USES=fortran to have them
|
2019-04-22 13:16:33 +00:00 |
|
tabixpp
|
biology/tabixpp: C++ wrapper to tabix indexer
|
2018-04-14 23:52:16 +00:00 |
|
treekin
|
New port: biology/treekin: Efficient computation of RNA folding dynamics
|
2019-06-15 20:37:06 +00:00 |
|
treepuzzle
|
|
|
|
trimadap
|
biology/trimadap: Mark only for amd64 and i386
|
2019-05-11 00:18:24 +00:00 |
|
trimmomatic
|
|
|
|
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
|
Clean up plist
|
2019-04-25 13:25:50 +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
|
|
|
|
vsearch
|
biology/vsearch: Update to 2.13.4
|
2019-05-11 13:42:33 +00:00 |
|
wise
|
|
|
|
Makefile
|
New port: biology/treekin: Efficient computation of RNA folding dynamics
|
2019-06-15 20:37:06 +00:00 |
47c6c8bc57