Jason W. Bacon 001947d3e5 biology/vsearch: Update to 2.22.1 ... Add the derep_smallmem command for dereplication with less memory usage Changes: https://github.com/torognes/vsearch/releases Reported by: portscout		2022-09-21 11:24:14 -05:00
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abyss	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ad2vcf	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
artemis	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
avida	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
babel	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bamtools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bamutil	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bbmap	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bcftools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bedtools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bfc	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bio-mocha	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bioawk	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
biococoa	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
biolibc	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
biolibc-tools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bioparser	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
biosig	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
biosoup	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
biostar-tools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bolt-lmm	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bowtie	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bowtie2	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
bwa	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
canu	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
cd-hit	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
cdbfasta	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
checkm	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
clustal-omega	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
clustalw	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
cufflinks	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
cytoscape	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ddocent	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
diamond	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
dsr-pdb	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
edlib	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
emboss	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
erminej	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
exonerate	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fasta	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fasta3	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastahack	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastdnaml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastool	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastp	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastq-trim	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastqc	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fasttree	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fastx-toolkit	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
figtree	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
flash	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
fluctuate	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
freebayes	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
garlic	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gatk	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gcta	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gemma	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
generand	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gff2ps	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gffread	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gmap	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
gperiodic	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
graphlan	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
groopm	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
haplohseq	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
hhsuite	biology/hhsuite: Broken on armv7	2022-09-09 14:49:50 -07:00
hisat2	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
hmmer	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
htslib	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
hyphy	biology/hyphy: Update to 2.5.42	2022-09-19 18:10:39 -03:00
igv	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
infernal	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
iolib	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
iqtree	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
jalview	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
jellyfish	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
kallisto	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
kmcp	all: Bump PORTREVISION after lang/go{118,119} update	2022-09-08 11:33:18 -05:00
lamarc	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libbigwig	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libgff	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libgtextutils	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libneurosim	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libnuml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libsbml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
libsedml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
linux-foldingathome	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
mafft	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
mapm3	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
migrate	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
minimap2	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
mmseqs2	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
molden	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
mothur	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
mrbayes	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
mummer	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
muscle	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ncbi-blast+	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ncbi-cxx-toolkit	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ncbi-entrez-direct	all: Bump PORTREVISION after lang/go{118,119} update	2022-09-08 11:33:18 -05:00
ncbi-toolkit	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ncbi-vdb	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ngs-sdk	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-AcePerl	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-ASN1-EntrezGene	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Cluster	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Coordinate	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Das	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Das-Lite	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-DB-EMBL	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-DB-NCBIHelper	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-FeatureIO	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-GFF3	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Glite	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Graphics	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-MAGETAB	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-NEXUS	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Phylo	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-SCF	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-Bio-Variation	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-BioPerl	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-BioPerl-Run	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-transdecoder	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
p5-TrimGalore	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
paml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
pbbam	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
pbseqan	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
peak-classifier	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
pear-merger	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
phrap	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
phred	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
phyml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
picard-tools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
plink	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
pooler	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
primer3	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
prodigal	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
prodigy-lig	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
protomol	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
psi88	Remove WWW lines that have been moved into Makefiles	2022-09-08 17:46:38 +02:00
py-bcbio-gff	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-biom-format	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-biopython	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-bx-python	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-crossmap	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-cutadapt	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-deeptools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-deeptoolsintervals	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-dna-features-viewer	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-dnaio	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-ete3	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-Genesis-PyAPI	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-gffutils	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-goatools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-gtfparse	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-hits	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-libnuml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-libsedml	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-loompy	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-macs2	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-mrcfile	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-multiqc	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-ont-fast5-api	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-orange3-bioinformatics	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-orange3-single-cell	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-pandas-charm	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-py2bit	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-pybigwig	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-pyfaidx	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-pysam	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-PySCeS	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-python-libsbml	*/*: Update path set in BUILD_DEPENDS for CMake	2022-09-09 22:32:24 +02:00
py-pywgsim	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-resdk	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-scikit-bio	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
py-xenaPython	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
pyfasta	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
python-nexus	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
rainbow	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
rampler	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
readseq	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
recombine	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ruby-bio	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
rubygem-bio	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
rubygem-bio-executables	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
rubygem-bio-old-biofetch-emulator	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
rubygem-bio-shell	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
sam2pairwise	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
samtools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
scrm	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seaview	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqan	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqan-apps	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqan1	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqan3	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqio	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
seqkit	all: Bump PORTREVISION after lang/go{118,119} update	2022-09-08 11:33:18 -05:00
seqtk	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
sigviewer	Mk/Uses: always use colon for build/run suffix	2022-09-11 12:20:14 +02:00
sim4	Remove WWW lines that have been moved into Makefiles	2022-09-08 17:46:38 +02:00
slclust	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
smithwaterman	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
snpeff	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
spoa	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
sra-tools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
stacks	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
star	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
stringtie	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
subread	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
tabixpp	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
taxonkit	all: Bump PORTREVISION after lang/go{118,119} update	2022-09-08 11:33:18 -05:00
treekin	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
treepuzzle	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
trimadap	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
trimmomatic	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
tRNAscan-SE	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ucsc-userapps	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
ugene	Mk/Uses: always use colon for build/run suffix	2022-09-11 12:20:14 +02:00
unikmer	all: Bump PORTREVISION after lang/go{118,119} update	2022-09-08 11:33:18 -05:00
vcf-split	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
vcf2hap	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
vcflib	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
vcftools	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
velvet	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
viennarna	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
vsearch	biology/vsearch: Update to 2.22.1	2022-09-21 11:24:14 -05:00
vt	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
wise	Remove WWW entries moved into port Makefiles	2022-09-07 23:58:51 +02:00
Makefile	biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching	2022-08-07 13:30:47 -07:00