| .. |
|
abyss
|
devel/boost-*: update to 1.71.0
|
2019-08-19 15:35:27 +00:00 |
|
artemis
|
|
|
|
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
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +00:00 |
|
bedtools
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
biology/bowtie2: Clarify CPU-specificity
|
2019-04-24 17:41:27 +00:00 |
|
bwa
|
|
|
|
canu
|
devel/boost-*: update to 1.71.0
|
2019-08-19 15:35:27 +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 |
|
chemeq
|
Mark BROKEN: unfetchable
|
2019-08-04 08:31:22 +00:00 |
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
consed
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +00:00 |
|
cufflinks
|
devel/boost-*: update to 1.71.0
|
2019-08-19 15:35:27 +00:00 |
|
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
|
2019-07-26 20:46:53 +00:00 |
|
diamond
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +00:00 |
|
dsr-pdb
|
devel/boost-*: update to 1.71.0
|
2019-08-19 15:35:27 +00:00 |
|
emboss
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +00:00 |
|
exonerate
|
New port: biology/exonerate: Generic tool for sequence alignment
|
2018-07-13 07:02:16 +00:00 |
|
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
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
fastqc
|
|
|
|
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
|
|
|
|
gatk
|
biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43
|
2019-07-26 18:03:08 +00:00 |
|
gemma
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
biology/gperiodic: fix NLS and other rough edges
|
2019-08-23 15:26:55 +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 |
|
hhsuite
|
biology/hhsuite: fix build on powerpc64
|
2019-08-05 14:23:23 +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
|
biology/htslib: update to 1.9
|
2018-08-02 19:27:13 +00:00 |
|
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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
kallisto
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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 |
|
linux-foldingathome
|
Mark BROKEN: unfetchable
|
2019-08-04 08:31:22 +00:00 |
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
minimap2
|
biology/minimap2: Upgrade to 2.17
|
2019-05-05 14:56:07 +00:00 |
|
molden
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
mopac
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
mothur
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
ncbi-toolkit
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +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 1.007005 (1.7.5)
|
2019-08-11 16:49:24 +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 0.6.1
|
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 1.71.0
|
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
|
|
|
|
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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
2019-07-26 20:46:53 +00:00 |
|
py-biom-format
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
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 2.3
|
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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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-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
|
biology/seaview: Fix build with Clang 6
|
2018-09-08 09:01:35 +00:00 |
|
seqan
|
|
|
|
seqan-apps
|
devel/boost-*: update to 1.71.0
|
2019-08-19 15:35:27 +00:00 |
|
seqan1
|
|
|
|
seqio
|
|
|
|
seqtk
|
|
|
|
seqtools
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +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
|
2019-07-26 20:46:53 +00:00 |
|
tabixpp
|
|
|
|
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
|
|
|
|
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
|
devel/boost-*: update to 1.71.0
|
2019-08-19 15:35:27 +00:00 |
|
vcflib
|
|
|
|
vcftools
|
biology/vcftools: Update to 0.1.16, a security release
|
2018-08-04 01:29:29 +00:00 |
|
velvet
|
|
|
|
viennarna
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
vsearch
|
biology/vsearch: Update to 2.13.4
|
2019-05-11 13:42:33 +00:00 |
|
wise
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +00:00 |
|
Makefile
|
New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)
|
2019-07-11 17:05:22 +00:00 |
