| .. |
|
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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
biococoa
|
Update Objective-C LLVM version to 6.0.
|
2018-09-26 15:23:37 +00:00 |
|
bowtie
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
bowtie2
|
Update devel/tbb to version 2019.1 and bump dependent ports' revisions
|
2018-10-11 14:47:13 +00:00 |
|
bwa
|
|
|
|
canu
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
cd-hit
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
cdbfasta
|
|
|
|
checkm
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +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 |
|
clustalx
|
Mark QT4 ports/functionality for removal on 2019-03-15
|
2018-12-02 15:41:47 +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 |
|
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
|
|
|
|
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 |
|
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
|
|
|
|
gperiodic
|
|
|
|
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
|
biology/hmmer: update to 3.2.1
|
2018-07-11 15:15:03 +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
|
devel/gradle: Update to 5.0
|
2018-12-04 17:53:46 +00:00 |
|
infernal
|
Allow building on powerpc64.
|
2018-09-27 23:02:56 +00:00 |
|
iolib
|
Remove the incorrect typedefs to fix build on tier-2.
|
2018-11-05 19:45:23 +00:00 |
|
iqtree
|
biology/iqtree: switch to outsource cmake build
|
2018-12-27 18:34:44 +00:00 |
|
jalview
|
|
|
|
jellyfish
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
kallisto
|
Update science/hdf5 to 1.10.4
|
2019-01-05 22:46:53 +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
|
|
|
|
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 2.1.0
|
2019-01-06 20:39:43 +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 2.1.0
|
2019-01-06 20:39:43 +00:00 |
|
ngs-sdk
|
biology/ngs-sdk: Update 2.9.2 -> 2.9.3
|
2018-10-18 21:38:21 +00:00 |
|
p5-AcePerl
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-ASN1-EntrezGene
|
Update to 1.73
|
2018-10-10 10:23:10 +00:00 |
|
p5-Bio-Coordinate
|
Fix every instance of RUN_DEPENDS:=${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 every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-NEXUS
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-Phylo
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-SCF
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-BioPerl
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-BioPerl-Run
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +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
|
|
|
|
paml
|
biology/paml: Set PORTVERSION directly
|
2018-04-26 15:36:30 +00:00 |
|
pbbam
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
pbcopper
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
pbseqan
|
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn
|
2018-04-21 17:21:30 +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
|
Change 4 ports from net/mpich2 to net/mpich
|
2018-09-22 18:00:24 +00:00 |
|
plinkseq
|
|
|
|
primer3
|
biology/primer3: Fix build with Clang 6
|
2018-08-25 03:35:46 +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 PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +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
|
biology/py-cutadapt: Upgrade to 1.18
|
2018-09-20 14:10:52 +00:00 |
|
py-fastTSNE
|
New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE
|
2018-12-15 08:58:05 +00:00 |
|
py-Genesis-PyAPI
|
Use PY_FLAVOR for dependencies.
|
2018-06-20 17:05:41 +00:00 |
|
py-gffutils
|
New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework
|
2018-10-19 02:06:53 +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
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +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
|
biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2
|
2018-10-28 04:34:14 +00:00 |
|
py-pysam
|
biology/py-pysam: Update 0.15.1 -> 0.15.2
|
2019-01-26 04:15:54 +00:00 |
|
pycogent
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +00:00 |
|
pyfasta
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2018-12-12 01:35:33 +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
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
Change cmake default behaviour to outsource.
|
2018-12-25 20:25:39 +00:00 |
|
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: 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
|
|
|
|
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
|
Change cmake default behaviour to outsource.
|
2018-12-25 20:25:39 +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
|
|
|
|
wise
|
|
|
|
Makefile
|
Sort categories Makefiles.
|
2019-01-22 16:26:49 +00:00 |
