| .. |
|
abyss
|
|
|
|
ad2vcf
|
biology/ad2vcf: Update to 0.1.5
|
2022-03-15 16:39:32 -05:00 |
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
*/*: Remove redundant '-*' from CONFLICTS definitions
|
2021-11-25 22:40:11 +01:00 |
|
bamtools
|
devel/jsoncpp: Update to 1.9.4 -> 1.9.5
|
2021-11-05 12:09:19 -07:00 |
|
bamutil
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
bbmap
|
|
|
|
bcftools
|
biology/bcftools: Update to 1.15
|
2022-02-26 09:04:10 -06:00 |
|
bedtools
|
|
|
|
bfc
|
|
|
|
bio-mocha
|
biology/bio-mocha: Update bcftools submodule to 1.15
|
2022-02-26 09:04:10 -06:00 |
|
bioawk
|
|
|
|
biococoa
|
|
|
|
biolibc
|
biology/biolibc: Update to 0.2.2
|
2022-03-15 16:35:22 -05:00 |
|
biolibc-tools
|
biology/biolibc-tools: Update to 0.1.2
|
2022-03-15 16:36:49 -05:00 |
|
bioparser
|
|
|
|
biosig
|
|
|
|
biosoup
|
|
|
|
biostar-tools
|
biology/biostar-tools: Allow package build on non-amd64 systems
|
2021-12-01 09:49:28 -06:00 |
|
bolt-lmm
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
bowtie
|
biology/bowtie: enable on riscv64
|
2021-12-15 13:55:57 +01:00 |
|
bowtie2
|
biology/bowtie2: Update to 2.4.5
|
2022-01-21 08:33:54 -06:00 |
|
bwa
|
biology/bwa: don't use GCC on powerpc64le
|
2021-12-01 17:34:18 +00:00 |
|
canu
|
biology/canu: fix CATEGORIES
|
2021-12-20 12:59:13 +00:00 |
|
cd-hit
|
biology/cd-hit: fix build on armv7
|
2021-11-21 13:26:44 +00:00 |
|
cdbfasta
|
|
|
|
checkm
|
|
|
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
cufflinks
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
cytoscape
|
|
|
|
ddocent
|
|
|
|
diamond
|
biology/diamond: Update to 2.0.14
|
2022-01-13 13:42:38 -04:00 |
|
dsr-pdb
|
|
|
|
edlib
|
|
|
|
emboss
|
*/*: Remove redundant '-[0-9]*' from CONFLICTS
|
2021-10-29 11:50:18 +02:00 |
|
erminej
|
|
|
|
exonerate
|
|
|
|
fasta
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
fasta3
|
|
|
|
fastahack
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
biology/fastp: Add USE_GCC to hack around seg faults
|
2022-01-21 10:16:01 -06:00 |
|
fastqc
|
|
|
|
fasttree
|
|
|
|
fastx-toolkit
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
figtree
|
|
|
|
flash
|
|
|
|
fluctuate
|
|
|
|
freebayes
|
biology/freebayes: Update to 1.3.6
|
2022-02-06 14:23:45 -06:00 |
|
garlic
|
|
|
|
gatk
|
|
|
|
gcta
|
|
|
|
gemma
|
math/gsl: bump portrevision of consumers after update to 2.7.1
|
2022-01-12 20:41:22 +01:00 |
|
generand
|
|
|
|
gff2ps
|
|
|
|
gffread
|
biology/gffread: remove local poudriere files
|
2022-03-07 23:44:38 +01:00 |
|
gmap
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
gperiodic
|
|
|
|
graphlan
|
|
|
|
groopm
|
|
|
|
haplohseq
|
|
|
|
hhsuite
|
biology/hhsuite: fix packaging on powerpc
|
2021-11-16 12:03:42 +00:00 |
|
hisat2
|
biology/hisat2: enable on riscv64
|
2021-12-16 22:38:56 +01:00 |
|
hmmer
|
|
|
|
htslib
|
biology/htslib: Update to 1.15
|
2022-02-26 09:04:10 -06:00 |
|
hyphy
|
biology/hyphy: Fix build with clang 13.0.0
|
2022-02-21 16:13:16 -04:00 |
|
igv
|
|
|
|
infernal
|
|
|
|
iolib
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
iqtree
|
|
|
|
jalview
|
|
|
|
jellyfish
|
*: Clean up some things
|
2021-10-12 17:01:38 +02:00 |
|
kallisto
|
biology/kallisto: Update to 0.48.0
|
2022-01-19 07:57:36 -06:00 |
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libgff
|
biology/libgff: GFF/GTF parsing library based on GCLib
|
2021-12-05 14:50:42 -06:00 |
|
libgtextutils
|
|
|
|
libneurosim
|
biology/libneurosim: New port: Common interfaces for neuronal simulators
|
2021-10-08 10:20:27 -07:00 |
|
libnuml
|
|
|
|
libsbml
|
biology/libsbml: Update WWW
|
2022-02-28 20:45:56 +08:00 |
|
libsedml
|
biology/{,py-}libsedml: Update 2.0.27 -> 2.0.28
|
2022-03-05 18:15:32 -08:00 |
|
linux-foldingathome
|
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
|
2021-10-25 12:58:29 +00:00 |
|
mafft
|
biology/mafft: Update to 7.267
|
2021-10-22 13:11:23 +08:00 |
|
mapm3
|
|
|
|
migrate
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
minimap2
|
biology/minimap2: Update to 2.24
|
2021-12-31 08:30:52 -06:00 |
|
mmseqs2
|
|
|
|
molden
|
*: Clean up some things
|
2022-01-17 14:20:25 +01:00 |
|
mopac
|
|
|
|
mothur
|
biology/mothur: Update 1.46.1 -> 1.47.0
|
2022-01-21 09:14:38 -08:00 |
|
mrbayes
|
|
|
|
mummer
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
muscle
|
|
|
|
ncbi-blast+
|
devel/grpc: Update to 1.44.0
|
2022-03-08 02:10:55 +08:00 |
|
ncbi-cxx-toolkit
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
ncbi-entrez-direct
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
ncbi-toolkit
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
ncbi-vdb
|
security/mbedtls: Update to 2.28.0 and fix make test
|
2022-01-28 13:14:09 +01:00 |
|
ngs-sdk
|
biology/ngs-sdk: Update 2.11.1 -> 2.11.2
|
2022-01-27 01:29:09 -08:00 |
|
p5-AcePerl
|
|
|
|
p5-Bio-ASN1-EntrezGene
|
|
|
|
p5-Bio-Cluster
|
|
|
|
p5-Bio-Coordinate
|
|
|
|
p5-Bio-Das
|
|
|
|
p5-Bio-Das-Lite
|
|
|
|
p5-Bio-DB-EMBL
|
|
|
|
p5-Bio-DB-NCBIHelper
|
|
|
|
p5-Bio-FeatureIO
|
|
|
|
p5-Bio-GFF3
|
|
|
|
p5-Bio-Glite
|
|
|
|
p5-Bio-Graphics
|
|
|
|
p5-Bio-MAGETAB
|
|
|
|
p5-Bio-NEXUS
|
|
|
|
p5-Bio-Phylo
|
|
|
|
p5-Bio-SCF
|
|
|
|
p5-Bio-Variation
|
|
|
|
p5-BioPerl
|
|
|
|
p5-BioPerl-Run
|
|
|
|
p5-transdecoder
|
|
|
|
p5-TrimGalore
|
|
|
|
paml
|
|
|
|
pbbam
|
*: fix tab vs. space issues, and comments according to the guide.
|
2021-10-16 11:51:39 +02:00 |
|
pbseqan
|
*: fix tab vs. space issues, and comments according to the guide.
|
2021-10-16 11:51:39 +02:00 |
|
peak-classifier
|
biology/peak-classifier: Update to 0.1.3
|
2022-03-15 16:41:51 -05:00 |
|
pear-merger
|
|
|
|
phrap
|
|
|
|
phred
|
|
|
|
phyml
|
biology/phyml: update to 3.3.20211231
|
2022-01-02 18:31:24 +01:00 |
|
picard-tools
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
plink
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
pooler
|
biology/pooler: Update to 1.84
|
2022-03-14 09:41:38 -05:00 |
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
|
|
|
protomol
|
|
|
|
psi88
|
|
|
|
py-bcbio-gff
|
biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)
|
2022-02-03 13:38:42 -06:00 |
|
py-biom-format
|
|
|
|
py-biopython
|
biology/py-biopython: Update to 1.79
|
2021-10-12 14:43:04 +08:00 |
|
py-bx-python
|
biology/py-bx-python: Update 0.8.11-6 -> 0.8.13
|
2021-12-21 01:03:57 -08:00 |
|
py-crossmap
|
biology/py-crossmap: chase ad5a0604c4
|
2021-10-14 00:53:16 +00:00 |
|
py-cutadapt
|
|
|
|
py-deeptools
|
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
|
2021-10-14 06:51:12 -05:00 |
|
py-deeptoolsintervals
|
biology/py-deeptoolsintervals: Python interface for deepTools interval trees
|
2021-10-13 11:02:13 -05:00 |
|
py-dna-features-viewer
|
biology/py-dna-features-viewer: Add missing dependency
|
2022-02-12 09:12:39 -06:00 |
|
py-dnaio
|
|
|
|
py-ete3
|
devel/py-qt5, devel/py-sip: Update versions
|
2022-03-07 18:39:13 +01:00 |
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
|
|
|
py-goatools
|
|
|
|
py-gtfparse
|
|
|
|
py-hits
|
|
|
|
py-libnuml
|
biology/py-libnuml: fix install with python 3.10+
|
2021-11-02 21:08:32 +03:00 |
|
py-libsedml
|
biology/{,py-}libsedml: Update 2.0.27 -> 2.0.28
|
2022-03-05 18:15:32 -08:00 |
|
py-loompy
|
biology/py-loompy: Update 3.0.6 -> 3.0.7
|
2022-03-06 09:09:59 -08:00 |
|
py-macs2
|
|
|
|
py-multiqc
|
|
|
|
py-ont-fast5-api
|
|
|
|
py-orange3-bioinformatics
|
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
|
2022-01-23 21:56:25 +01:00 |
|
py-orange3-single-cell
|
cleanup: remove transitive py27 deprecation (www/qt5-webengine)
|
2022-01-23 21:56:25 +01:00 |
|
py-pandas-charm
|
|
|
|
py-py2bit
|
biology/py-py2bit: Python interface for 2bit packed nucleotide files
|
2021-10-13 07:53:53 -05:00 |
|
py-pybigwig
|
biology/py-bigwig: Rename to biology/py-pybigwig
|
2021-10-13 16:21:32 -05:00 |
|
py-pyfaidx
|
|
|
|
py-pysam
|
biology/py-pysam: Update 0.16.0.1 -> 0.18.0
|
2021-12-19 23:48:52 -08:00 |
|
py-PySCeS
|
biology/py-PySCeS: fix with Python ≠ 3.8
|
2022-03-02 19:49:25 +01:00 |
|
py-python-libsbml
|
biology/py-python-libsbml: limit supported python versions, fix build
|
2021-11-03 21:26:41 +03:00 |
|
py-pywgsim
|
|
|
|
py-resdk
|
biology/py-resdk: Update 13.8.0 -> 14.0.0
|
2022-01-19 10:10:01 -08:00 |
|
py-scikit-bio
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
py-xenaPython
|
|
|
|
pyfasta
|
|
|
|
python-nexus
|
|
|
|
rainbow
|
|
|
|
rampler
|
|
|
|
readseq
|
|
|
|
recombine
|
|
|
|
ruby-bio
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
rubygem-bio
|
biology/rubygem-bio: Update to 2.0.3
|
2022-01-12 02:47:28 +08:00 |
|
rubygem-bio-executables
|
|
|
|
rubygem-bio-old-biofetch-emulator
|
|
|
|
rubygem-bio-shell
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
sam2pairwise
|
|
|
|
samtools
|
biology/samtools: Update to 1.15
|
2022-02-26 09:04:10 -06:00 |
|
scrm
|
|
|
|
seaview
|
biology/seaview: Update version 5.0.4=>5.0.5
|
2021-12-05 19:02:42 -06:00 |
|
seqan
|
*/*: Remove redundant '-[0-9]*' from CONFLICTS
|
2021-10-29 11:50:18 +02:00 |
|
seqan1
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
seqan3
|
biology/seqan3: Update 3.0.3 -> 3.1.0
|
2021-11-14 21:18:53 -08:00 |
|
seqan-apps
|
|
|
|
seqio
|
|
|
|
seqkit
|
biology/seqkit: Update 2.0.1 -> 2.1.0
|
2021-11-16 10:57:47 -08:00 |
|
seqtk
|
biology/seqtk: Update to 1.3
|
2021-12-18 13:37:06 -06:00 |
|
sigviewer
|
|
|
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
snpeff
|
|
|
|
spoa
|
devel/cpu_features: Install cmake files, install headers into a dedicated directory
|
2022-01-26 08:45:29 -08:00 |
|
sra-tools
|
Fix CONFLICTS entries of multiple ports
|
2022-01-10 16:15:39 +01:00 |
|
stacks
|
|
|
|
star
|
biology/star: Update to 2.7.9a
|
2021-11-26 15:57:02 -06:00 |
|
stringtie
|
|
|
|
subread
|
|
|
|
tabixpp
|
|
|
|
taxonkit
|
biology/taxonkit: Update 0.9.0 -> 0.10.1
|
2022-02-27 10:35:41 -08:00 |
|
treekin
|
biology/treekin: Unbreak
|
2021-10-15 08:50:24 -07:00 |
|
treepuzzle
|
|
|
|
trimadap
|
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
|
2021-10-25 12:58:29 +00:00 |
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ucsc-userapps
|
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
|
2021-10-25 12:58:29 +00:00 |
|
ugene
|
biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).
|
2021-10-14 11:23:37 +00:00 |
|
unikmer
|
|
|
|
vcf2hap
|
biology/vcf2hap: Update to 0.1.5
|
2022-03-15 16:45:04 -05:00 |
|
vcf-split
|
biology/vcf-split: Update to 0.1.4
|
2022-03-15 16:43:40 -05:00 |
|
vcflib
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
Update CONFLICTS definitions in categories a* to c*
|
2022-02-06 19:36:07 +01:00 |
|
vsearch
|
biology/vsearch: Update to 2.21.1
|
2022-01-23 16:32:43 -06:00 |
|
vt
|
|
|
|
wise
|
|
|
|
Makefile
|
biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)
|
2022-02-03 13:38:42 -06:00 |
