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freebsd-ports/biology
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Felix Palmen ddae4e92d8 Mk/Uses: always use colon for build/run suffix 
Most USES use a colon for build/run(/test) suffixes. Change kde.mk,
qt.mk and pyqt.mk to do the same, and update all ports using that.

Document in CHANGES.

PR:			266034
Exp-run by:		antoine
Approved by:		tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D36349
2022-09-11 12:20:14 +02:00
..
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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
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
seqan-apps 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
vcf2hap Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
vcf-split 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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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