| .. |
|
abyss
|
Chanse update of devel/libffi
|
2020-07-04 18:11:42 +00:00 |
|
artemis
|
Clean up after java/openjdk6 and java/openjdk6-jre removal
|
2019-11-26 21:46:12 +00:00 |
|
avida
|
biology/avida: unbreak on powerpc64
|
2019-10-23 16:25:10 +00:00 |
|
babel
|
|
|
|
bamtools
|
Bump devel/jsoncpp consumers after r540853.
|
2020-06-30 17:46:18 +00:00 |
|
bcftools
|
biology/bcftools: Upgrade to 1.10.2
|
2020-08-03 18:16:54 +00:00 |
|
bedtools
|
biology/bedtools: Upgrade to 2.29.2
|
2019-12-19 01:04:11 +00:00 |
|
bioawk
|
biology/bioawk: BWK awk modified for biological data
|
2020-06-05 02:45:33 +00:00 |
|
biococoa
|
Return theraven's ports to the pool after safekeeping his commit bit.
|
2020-03-05 20:49:05 +00:00 |
|
bolt-lmm
|
Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
|
2020-05-06 16:11:14 +00:00 |
|
bowtie
|
biology/bowtie: Unbreak build with GCC 10
|
2020-07-04 10:46:08 +00:00 |
|
bowtie2
|
Update devel/tbb to 2020.3 and bump dependent ports' revisions
|
2020-07-17 10:12:25 +00:00 |
|
bwa
|
|
|
|
canu
|
Mark as BROKEN on powerpc64:
|
2020-05-17 02:25:16 +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
|
|
|
|
cufflinks
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
cytoscape
|
Clean up after java/openjdk6 and java/openjdk6-jre removal
|
2019-11-26 21:46:12 +00:00 |
|
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 2.0.2
|
2020-08-07 11:20:11 +00:00 |
|
dsr-pdb
|
devel/boost-*: update to 1.72.0
|
2019-12-11 17:53:48 +00:00 |
|
emboss
|
- update libgd to 2.3.0
|
2020-05-04 21:31:39 +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
|
biology/fastp: Upgrade to 0.20.1
|
2020-04-09 16:17:02 +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 4.1.7.0 -> 4.1.8.0
|
2020-07-09 00:40:56 +00:00 |
|
gcta
|
Bump 46 ports depending on math/openblas because the after the recent math/openblas update the library name changed in openblas.
|
2020-05-06 16:11:14 +00:00 |
|
gemma
|
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
|
2020-05-06 16:39:12 +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
|
- Update WWW
|
2020-01-19 09:30:22 +00:00 |
|
graphlan
|
Deprecate a few ports
|
2020-02-23 15:25:53 +00:00 |
|
grappa
|
|
|
|
groopm
|
Deprecate a few ports
|
2020-02-23 15:25:53 +00:00 |
|
haplohseq
|
Deprecate some ports using deprecated version of python
|
2020-03-08 17:01:46 +00:00 |
|
hhsuite
|
biology/hhsuite: fix build on powerpc64 elfv2
|
2020-05-11 19:33:32 +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 3.3
|
2020-01-29 05:55:12 +00:00 |
|
htslib
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
hyphy
|
biology/hyphy: Update to version 2.5.15
|
2020-06-28 16:40:33 +00:00 |
|
igv
|
Deprecate java/openjfx8-devel consumers
|
2020-03-19 09:33:13 +00:00 |
|
infernal
|
biology/infernal: update to 1.1.3
|
2020-01-27 17:57:14 +00:00 |
|
iolib
|
- Fix build in head i386
|
2019-04-01 19:33:15 +00:00 |
|
iqtree
|
biology/iqtree: Update to version 2.0.6
|
2020-05-30 18:43:26 +00:00 |
|
jalview
|
Clean up after java/openjdk6 and java/openjdk6-jre removal
|
2019-11-26 21:46:12 +00:00 |
|
jellyfish
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
kallisto
|
biology/kallisto: Revert to 0.46.1
|
2020-08-03 15:45:21 +00:00 |
|
lagan
|
Convert to UCL & cleanup pkg-message (categories a-c)
|
2019-08-13 16:00:39 +00:00 |
|
lamarc
|
|
|
|
libbigwig
|
New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)
|
2019-07-11 17:05:22 +00:00 |
|
libgtextutils
|
|
|
|
libsbml
|
Move devel/swig30 to devel/swig and update to 4.0.1
|
2020-06-17 18:17:45 +00:00 |
|
linux-foldingathome
|
Update to 7.6.13
|
2020-05-09 13:21:29 +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
|
Update devel/gmake to 4.3.
|
2020-05-09 19:24:49 +00:00 |
|
mrbayes
|
- Swap back from net/openmpi3 to net/openmpi
|
2020-04-21 21:47:57 +00:00 |
|
mummer
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
muscle
|
biology/muscle: unbreak in -CURRENT
|
2020-01-17 16:49:03 +00:00 |
|
ncbi-blast+
|
Bump PORTREVISION for security/nettle shlib change
|
2020-05-16 10:51:32 +00:00 |
|
ncbi-cxx-toolkit
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
ncbi-toolkit
|
Bump PORTREVISION for security/nettle shlib change
|
2020-05-16 10:51:32 +00:00 |
|
ngs-sdk
|
biology/ngs-sdk: Update 2.10.4 -> 2.10.5
|
2020-04-04 20:09:00 +00:00 |
|
p5-AcePerl
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-ASN1-EntrezGene
|
Update *_DEPENDS
|
2020-01-08 18:36:30 +00:00 |
|
p5-Bio-Cluster
|
Update *_DEPENDS
|
2019-12-08 16:57:18 +00:00 |
|
p5-Bio-Coordinate
|
Cosmetic change
|
2020-04-02 12:01:30 +00:00 |
|
p5-Bio-Das
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-Das-Lite
|
Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except
|
2018-10-06 13:06:42 +00:00 |
|
p5-Bio-DB-EMBL
|
Add p5-Bio-DB-EMBL 1.7.4
|
2019-12-08 16:49:19 +00:00 |
|
p5-Bio-DB-NCBIHelper
|
Add p5-Bio-DB-NCBIHelper 1.7.6
|
2019-12-08 16:49:25 +00:00 |
|
p5-Bio-FeatureIO
|
Cosmetic change
|
2020-04-02 12:01:35 +00:00 |
|
p5-Bio-GFF3
|
Fix every instance of RUN_DEPENDS:=${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-Bio-Variation
|
Update to 1.7.5
|
2020-01-08 18:36:35 +00:00 |
|
p5-BioPerl
|
Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
|
2020-06-26 11:55:23 +00:00 |
|
p5-BioPerl-Run
|
Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago
|
2020-01-08 18:36:40 +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 0.6.5
|
2019-11-26 16:20:12 +00:00 |
|
paml
|
biology/paml: Update to version 4.9j
|
2019-11-22 15:32:40 +00:00 |
|
pbbam
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
pbcopper
|
Deprecate ports broken for more than 6 months
|
2020-07-26 07:32:00 +00:00 |
|
pbseqan
|
biology/unanimity and dependencies: Flag as no longer open source
|
2019-11-24 15:53:00 +00:00 |
|
pear-merger
|
|
|
|
phrap
|
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
|
2020-05-27 11:59:13 +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 3.3.20200621
|
2020-07-10 09:45:48 +00:00 |
|
picard-tools
|
biology/picard-tools: CLI tools for manipulating sequencing data
|
2020-06-13 13:54:47 +00:00 |
|
plink
|
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
|
2020-05-06 16:39:12 +00:00 |
|
primer3
|
|
|
|
prodigal
|
biology/prodigal: Eliminate a very old version from the portscout discovery process
|
2019-10-12 15:40:21 +00:00 |
|
prodigy-lig
|
Unbreak bulk -a
|
2020-06-13 15:05:44 +00:00 |
|
protomol
|
Add USES=xorg USES=gl, ports categories b
|
2019-11-04 21:08:20 +00:00 |
|
psi88
|
biology/psi88: Unbreak build with GCC 10
|
2020-07-04 12:15:58 +00:00 |
|
py-biom-format
|
Deprecate a few ports
|
2020-02-23 15:25:53 +00:00 |
|
py-biopython
|
biology/py-biopython: Set python requirement to 3.6+
|
2020-06-13 13:42:12 +00:00 |
|
py-bx-python
|
biology/py-bx-python: Update 0.8.8 -> 0.8.9
|
2020-06-26 04:17:11 +00:00 |
|
py-cutadapt
|
biology/py-cutadapt: Upgrade to 2.7
|
2019-11-23 14:45:53 +00:00 |
|
py-dnaio
|
biology/py-dnaio: Upgrade to 0.4.2
|
2020-05-24 15:23:15 +00:00 |
|
py-ete3
|
New port: biology/py-ete3: Framework for the analysis and visualization of trees
|
2020-05-16 00:13:09 +00:00 |
|
py-fastTSNE
|
Drop dependency on devel/openmp
|
2020-03-08 21:56:36 +00:00 |
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
Unbreak bulk -a
|
2020-07-14 07:59:28 +00:00 |
|
py-gtfparse
|
biology/py-gtfparse: Update 1.2.0 -> 1.2.1
|
2020-08-07 04:13:00 +00:00 |
|
py-hits
|
New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
|
2020-05-16 03:11:05 +00:00 |
|
py-loompy
|
biology/py-loompy: Update 2.0.17 -> 3.0.6
|
2020-06-16 02:26:08 +00:00 |
|
py-macs2
|
biology/py-macs2: Upgrade to 2.2.7.1
|
2020-04-14 12:13:55 +00:00 |
|
py-multiqc
|
biology/py-multiqc: Upgrade to 1.8
|
2019-11-26 16:25:08 +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
|
Update Sphinx
|
2020-05-11 23:51:58 +00:00 |
|
py-pandas-charm
|
Clean up some things
|
2020-05-30 00:57:02 +00:00 |
|
py-pyfaidx
|
Bump a few PORTREVISIONs after r498529
|
2019-04-10 06:18:31 +00:00 |
|
py-pysam
|
biology/py-pysam: Update 0.15.4 -> 0.16.0
|
2020-06-09 05:03:48 +00:00 |
|
py-scikit-bio
|
biology/py-scikit-bio: Fix license
|
2020-05-16 02:29:20 +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 |
|
pyfasta
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2019-07-26 20:46:53 +00:00 |
|
python-nexus
|
|
|
|
rainbow
|
Update WWW
|
2020-03-31 23:18:09 +00:00 |
|
recombine
|
Fix after gets(3) retirement using gets_s(3).
|
2019-09-02 05:00:43 +00:00 |
|
ruby-bio
|
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
|
2020-05-05 14:22:09 +00:00 |
|
rubygem-bio
|
Update to 2.0.1
|
2020-07-24 07:49:43 +00:00 |
|
rubygem-bio-executables
|
Add rubygem-bio-executables 1.0.0
|
2020-07-24 07:08:00 +00:00 |
|
rubygem-bio-old-biofetch-emulator
|
Add rubygem-bio-old-biofetch-emulator 1.0.0
|
2020-07-24 07:08:05 +00:00 |
|
rubygem-bio-shell
|
Add rubygem-bio-shell 1.0.0
|
2020-07-24 07:08:11 +00:00 |
|
samtools
|
biology/samtools: Upgrade to 1.10
|
2020-08-03 18:22:06 +00:00 |
|
scrm
|
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
|
2020-05-15 07:30:34 +00:00 |
|
seaview
|
biology/seaview: Update version 5.0.3=>5.0.4
|
2020-06-22 17:34:44 +00:00 |
|
seqan
|
|
|
|
seqan1
|
Fix some misspelled or duplicated LICENSE_*
|
2019-09-17 19:21:45 +00:00 |
|
seqan-apps
|
devel/boost-*: update to 1.72.0
|
2019-12-11 17:53:48 +00:00 |
|
seqio
|
|
|
|
seqtk
|
|
|
|
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 2.7.3a
|
2020-04-09 12:43:03 +00:00 |
|
stringtie
|
biology/stringtie: fix build on GCC architectures
|
2020-02-23 10:52:44 +00:00 |
|
subread
|
biology/subread: Read alignment, quantification and mutation discovery
|
2020-06-05 01:55:49 +00:00 |
|
tabixpp
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
tophat
|
Deprecate some ports using deprecated version of python
|
2020-03-08 17:01:46 +00:00 |
|
treekin
|
Fix math/openblas and bump dependent ports
|
2020-01-30 14:17:44 +00:00 |
|
treepuzzle
|
|
|
|
trimadap
|
biology/trimadap: Mark only for amd64 and i386
|
2019-05-11 00:18:24 +00:00 |
|
trimmomatic
|
Clean up after java/openjdk6 and java/openjdk6-jre removal
|
2019-11-26 21:46:12 +00:00 |
|
tRNAscan-SE
|
biology/tRNAscan-SE: update to 2.0.5
|
2020-01-13 17:36:57 +00:00 |
|
ugene
|
biology/ugene: prepare for Qt5-5.15
|
2020-05-19 18:00:02 +00:00 |
|
vcflib
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
- update libgd to 2.3.0
|
2020-05-04 21:31:39 +00:00 |
|
vsearch
|
biology/vsearch: Update to 2.15.0
|
2020-06-20 14:31:59 +00:00 |
|
vt
|
biology/vt: Patch to work with htslib 1.10.2
|
2020-08-03 17:42:32 +00:00 |
|
wise
|
a-b: Add missing USES={gnome,php,sdl,xorg}
|
2019-11-08 09:27:56 +00:00 |
|
Makefile
|
Add rubygem-bio-shell 1.0.0
|
2020-07-24 07:08:11 +00:00 |
