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freebsd-ports/biology
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Stefan Eßer b7f05445c0 Add WWW entries to port Makefiles 
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)
2022-09-07 23:10:59 +02:00
..
abyss Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ad2vcf Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
artemis Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
avida Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
babel Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bamtools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bamutil Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bbmap Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bcftools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bedtools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bfc Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bio-mocha Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bioawk Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
biococoa Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
biolibc Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
biolibc-tools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bioparser Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
biosig Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
biosoup Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
biostar-tools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bolt-lmm Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bowtie Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bowtie2 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
bwa Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
canu Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
cd-hit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
cdbfasta Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
checkm Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
clustal-omega Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
clustalw Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
cufflinks Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
cytoscape Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ddocent Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
diamond Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
dsr-pdb Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
edlib Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
emboss Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
erminej Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
exonerate Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fasta Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fasta3 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastahack Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastdnaml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastool Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastp Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastq-trim Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastqc Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fasttree Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fastx-toolkit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
figtree Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
flash Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
fluctuate Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
freebayes Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
garlic Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gatk Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gcta Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gemma Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
generand Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gff2ps Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gffread Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gmap Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
gperiodic Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
graphlan Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
groopm Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
haplohseq Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
hhsuite Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
hisat2 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
hmmer Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
htslib Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
hyphy Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
igv Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
infernal Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
iolib Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
iqtree Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
jalview Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
jellyfish Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
kallisto Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
kmcp Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
lamarc Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libbigwig Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libgff Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libgtextutils Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libneurosim Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libnuml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libsbml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
libsedml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
linux-foldingathome Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
mafft Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
mapm3 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
migrate Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
minimap2 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
mmseqs2 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
molden Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
mothur Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
mrbayes Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
mummer Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
muscle Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ncbi-blast+ Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ncbi-cxx-toolkit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ncbi-entrez-direct Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ncbi-toolkit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ncbi-vdb Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ngs-sdk Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-AcePerl Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-ASN1-EntrezGene Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Cluster Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Coordinate Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Das Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Das-Lite Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-DB-EMBL Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-DB-NCBIHelper Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-FeatureIO Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-GFF3 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Glite Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Graphics Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-MAGETAB Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-NEXUS Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Phylo Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-SCF Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-Bio-Variation Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-BioPerl Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-BioPerl-Run Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-transdecoder Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
p5-TrimGalore Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
paml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
pbbam Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
pbseqan Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
peak-classifier Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
pear-merger Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
phrap Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
phred Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
phyml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
picard-tools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
plink Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
pooler Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
primer3 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
prodigal Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
prodigy-lig Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
protomol Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
psi88 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
py-bcbio-gff Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-biom-format Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-biopython Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-bx-python Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-crossmap Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-cutadapt Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-deeptools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-deeptoolsintervals Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-dna-features-viewer Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-dnaio Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-ete3 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-Genesis-PyAPI Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-gffutils Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-goatools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-gtfparse Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-hits Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-libnuml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-libsedml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-loompy Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-macs2 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-mrcfile Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-multiqc Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-ont-fast5-api Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-orange3-bioinformatics Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-orange3-single-cell Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-pandas-charm Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-py2bit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-pybigwig Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-pyfaidx Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-pysam Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-PySCeS Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-python-libsbml Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-pywgsim Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-resdk Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-scikit-bio Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
py-xenaPython Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
pyfasta Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
python-nexus Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
rainbow Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
rampler Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
readseq Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
recombine Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ruby-bio Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
rubygem-bio Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
rubygem-bio-executables Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
rubygem-bio-old-biofetch-emulator Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
rubygem-bio-shell Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
sam2pairwise Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
samtools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
scrm Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seaview Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqan Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqan1 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqan3 Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqan-apps Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqio Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqkit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
seqtk Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
sigviewer Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
sim4 biology: remove 'Created by' lines 2022-07-20 16:20:57 +02:00
slclust Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
smithwaterman Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
snpeff Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
spoa Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
sra-tools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
stacks Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
star Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
stringtie Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
subread Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
tabixpp Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
taxonkit Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
treekin Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
treepuzzle Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
trimadap Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
trimmomatic Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
tRNAscan-SE Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ucsc-userapps Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
ugene Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
unikmer Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
vcf2hap Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
vcf-split Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
vcflib Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
vcftools Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
velvet Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
viennarna Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
vsearch Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
vt Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
wise Add WWW entries to port Makefiles 2022-09-07 23:10:59 +02:00
Makefile biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching 2022-08-07 13:30:47 -07:00