..
abyss
biology/abyss: Update 2.2.4 -> 2.2.5
2020-09-27 06:59:05 +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
Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.
2020-09-27 07:41:33 +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
biology/bwa: fix build on recent current
2020-08-28 11:17:13 +00:00
canu
biology/canu: Upgrade to 2.1
2020-09-14 22:27:37 +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/cufflinks: fix build on recent current
2020-08-28 18:24:04 +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 2.0.4
2020-08-30 16:14:22 +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
fluctuate
freebayes
Fix build with -fno-common
2020-09-21 18:14:57 +00:00
garlic
Add USES=xorg USES=gl, ports categories b
2019-11-04 21:08:20 +00:00
gatk
biology/gatk: Fix build
2020-09-08 19:25:36 +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
gmap
biology/gmap: Upgrade to 2020.09.12
2020-09-22 00:55:39 +00:00
gperiodic
- Update WWW
2020-01-19 09:30:22 +00:00
graphlan
biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed
2020-08-14 04:59:29 +00:00
grappa
Extend expiration of ports broken with -fno-common
2020-08-30 09:47:49 +00:00
groopm
biology/groopm: Remove python's 2.7 restriction placed here by mistake
2020-08-13 19:19:23 +00:00
hhsuite
biology/hhsuite: Update 3.2.0 -> 3.3.0
2020-08-27 04:28:24 +00:00
hisat2
hmmer
Also enable on powerpc64le.
2020-09-24 20:29:35 +00:00
htslib
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
hyphy
biology/hyphy: Update to version 2.5.18 and add AVX option
2020-09-02 17:47:10 +00:00
igv
Deprecate java/openjfx8-devel consumers
2020-03-19 09:33:13 +00:00
infernal
Also enable on powerpc64le.
2020-09-24 20:38:59 +00:00
iolib
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
Extend expiration of ports broken with -fno-common
2020-08-30 09:47:49 +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
Convert REINPLACE_CMD to patch file
2020-09-29 18:23:04 +00:00
linux-foldingathome
Update to 7.6.13
2020-05-09 13:21:29 +00:00
mafft
mapm3
biology/mapm3: Reformat patches.
2020-09-04 12:24:23 +00:00
migrate
minimap2
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+
Chase security/p11-kit update
2020-08-30 03:10:23 +00:00
ncbi-cxx-toolkit
biology/ncbi-cxx-toolkit: Fix build on 13
2020-09-27 04:57:44 +00:00
ncbi-toolkit
Chase security/p11-kit update
2020-08-30 03:10:23 +00:00
ngs-sdk
biology/ngs-sdk: Update 2.10.4 -> 2.10.5
2020-04-04 20:09:00 +00:00
p5-AcePerl
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
p5-Bio-Das-Lite
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
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
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: fix the build with LLVM 11
2020-08-20 17:07:03 +00:00
pbbam
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +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
Extend expiration of ports broken with -fno-common
2020-08-30 09:47:49 +00:00
phyml
biology/phyml: fix build on recent current
2020-08-29 08:34:27 +00:00
picard-tools
biology/picard-tools: Remove extraneous file
2020-08-30 14:06:54 +00:00
plink
Allow building on powerpc64le.
2020-09-27 07:44:15 +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
biology/py-biom-format: Fix fetch and relax scipy requirement
2020-09-26 09:10:37 +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
Update PyQt to 5.15.0, py-sip to 4.19.24 and qscintilla2 to 2.11.5
2020-10-05 15:50:03 +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
Unbreak bulk -a
2020-09-19 14:15:42 +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
biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1
2020-09-13 19:05:30 +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 build on the i386 architecture
2020-09-24 23:16:26 +00:00
py-xenaPython
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: Add -fcommon for clang 11
2020-09-18 00:57:35 +00:00
tabixpp
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
treekin
Fix math/openblas and bump dependent ports
2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
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
biology/viennarna: Update 2.4.14 -> 2.4.15
2020-09-07 21:49:07 +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
biology/py-biom-format: Restore in preparation for an update to v2.1.8
2020-09-24 19:31:43 +00:00
2933bb22c3