Rene Ladan 4e051b961c biology/gffread: remove local poudriere files		2022-03-07 23:44:38 +01:00
..
abyss
ad2vcf	biology/ad2vcf: Update to 0.1.4	2021-12-14 13:45:31 -06:00
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 0.2.1	2021-12-14 13:45:31 -06:00
biolibc-tools	biology/biolibc-tools: Update to 0.1.1	2021-12-14 13:45:32 -06:00
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 0.1.2	2021-12-14 13:45:32 -06:00
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 1.82	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	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	*/*: Remove compiler:openmp from Mk/Uses/compiler.mk	2021-10-03 19:47:27 +02:00
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 0.1.4	2021-12-14 13:45:32 -06:00
vcf-split	biology/vcf-split: Update to 0.1.3.3	2021-12-14 13:45:32 -06:00
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