Rene Ladan 4e051b961c biology/gffread: remove local poudriere files		2022-03-07 23:44:38 +01:00
..
abyss
ad2vcf
artemis
avida
babel
bamtools
bamutil
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
biolibc-tools
bioparser
biosig
biosoup
biostar-tools
bolt-lmm	Update CONFLICTS definitions in categories a* to c*	2022-02-06 19:36:07 +01:00
bowtie
bowtie2
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
cytoscape
ddocent
diamond
dsr-pdb
edlib
emboss
erminej
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
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
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
hisat2
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
kallisto
lamarc
libbigwig
libgff
libgtextutils
libneurosim
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
mafft
mapm3
migrate	Update CONFLICTS definitions in categories a* to c*	2022-02-06 19:36:07 +01:00
minimap2
mmseqs2
molden
mopac
mothur	biology/mothur: Update 1.46.1 -> 1.47.0	2022-01-21 09:14:38 -08:00
mrbayes
mummer
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
pbseqan
peak-classifier
pear-merger
phrap
phred
phyml
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 1.82	2022-02-10 15:23:48 +01:00
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
py-bx-python
py-crossmap
py-cutadapt
py-deeptools
py-deeptoolsintervals
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
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
py-pybigwig
py-pyfaidx
py-pysam
py-PySCeS	biology/py-PySCeS: fix with Python ≠ 3.8	2022-03-02 19:49:25 +01:00
py-python-libsbml
py-pywgsim
py-resdk
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
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
sam2pairwise
samtools	biology/samtools: Update to 1.15	2022-02-26 09:04:10 -06:00
scrm
seaview
seqan
seqan1	Update CONFLICTS definitions in categories a* to c*	2022-02-06 19:36:07 +01:00
seqan3
seqan-apps
seqio
seqkit
seqtk
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
stacks
star
stringtie
subread
tabixpp
taxonkit	biology/taxonkit: Update 0.9.0 -> 0.10.1	2022-02-27 10:35:41 -08:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps
ugene
unikmer
vcf2hap
vcf-split
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