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freebsd-ports/biology
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Muhammad Moinur Rahman 18c6e18276 Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 
Switch from Mk/bsd.ruby.mk to Mk/Uses/ruby.mk

Notable changes are.

- Mk/bsd.ruby.mk is moved to Mk/Uses/ruby.mk.
- USE_RUBY=yes is replaced with USES=ruby.
- USE_RUBY_EXTCONF is replaced with USES=ruby:extconf.
- USE_RUBY_RDOC is replaced with USES=ruby:rdoc.
- USE_RUBY_SETUP is replaces with USES=ruby:setup.
- RUBY_NO_BUILD_DEPENDS and RUBY_NO_RUN_DEPENDS are replaced with
  USES=ruby:{build,none,run}.
- RUBY_REQUIRE isn't used anywhere, so removed.
- USES=gem now implies USES=ruby.

This is mainly the work of yasu@ at https://reviews.freebsd.org/D27863

I have just made some cosmetic changes and ran exp-run to test that the
tree is not in a BROKEN state.

Approved by:	portmgr
Differential Revision:	https://reviews.freebsd.org/D37925
2023-01-14 17:08:33 -06:00
..
abyss
ad2vcf
artemis
atac-seq biology/atac-seq: Update to 0.1.1 2023-01-12 13:00:03 -06:00
augustus biology/augustus: New port: Genome annotation tool 2022-11-25 15:55:09 -08:00
avida
babel
bamtools
bamutil
barrnap biology/barrnap: Update descr 2022-11-24 19:12:18 -08:00
bbmap
bcftools biology/bcftools: Update to 1.16 2023-01-05 17:19:22 -06:00
bedtools
bfc
bio-mocha biology/bio-mocha: Update to 1.16 2023-01-05 17:21:03 -06:00
bioawk
biococoa
biolibc biology/biolibc: Update to 0.2.4 2022-12-11 14:06:23 -06:00
biolibc-tools biology/biolibc-tools: Update to 0.1.4.1 2022-12-13 18:11:56 -06:00
bioparser
biosig biology/biosig: Update 2.4.3 -> 2.5.0 2022-12-30 00:32:02 -08:00
biosoup biology/biosoup: Update g20201216 -> 0.10.0-2 2022-10-10 23:10:56 -07:00
biostar-tools
bolt-lmm
bowtie
bowtie2 biology/bowtie2: fix build on powerpc64* 2022-11-09 23:50:41 +01:00
bwa
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
cytoscape biology/cytoscape: Broken on armv6, armv7 2022-12-10 23:41:04 -08:00
ddocent
diamond
dsr-pdb
edlib
emboss
erminej
exonerate
fasda biology/fasda: Fast and simple differential analysis 2022-12-12 11:17:22 -06:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastq-trim biology/fastq-trim: Update to 0.1.2 2022-12-11 15:24:05 -06:00
fastqc
fasttree
fastx-toolkit
figtree
flash
fluctuate
freebayes biology/freebayes: Bump PORTREVISION for biology/htslib update 2023-01-05 19:22:33 -06:00
garlic
gatk biology/gatk: Update 4.2.6.1 -> 4.3.0.0 2022-11-26 20:06:47 -08:00
gcta
gemma
generand
gff2ps
gffread
gmap
gperiodic
graphlan
groopm */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
haplohseq
hhsuite
hisat2
hmmer biology/hmmer: Update to 3.3.2 2022-10-11 15:13:01 -05:00
htslib biology/htslib: Update to 1.16 2023-01-05 17:16:08 -06:00
hyphy biology/hyphy: Update to upstream tag 2.5.46hf1 2023-01-09 22:05:57 -04:00
igv
infernal biology/infernal: Update to 1.1.4 2022-10-12 11:15:54 +01:00
iolib
iqtree
jalview biology/jalview: Update 2.11.1.4 -> 2.11.2.5 2022-10-11 23:58:18 -07:00
jellyfish biology/jellyfish: Bump PORTREVISION for biology/htslib update 2023-01-05 19:24:44 -06:00
kallisto
kmcp all: Bump PORTVERSION after lang/go{118,119} update 2023-01-14 06:31:17 -05:00
lamarc biology/lamarc: Refactor after wxgtk28 removal 2022-12-31 04:54:58 +01:00
libbigwig
libcombine biology/libcombine: Update 0.2.19 -> 0.2.20 2022-12-08 03:11:24 -08:00
libgff
libgtextutils
libneurosim
libnuml
libsbml
libsedml
linux-foldingathome
mafft
mapm3
megahit biology/megahit: Add cmake patch to respect ports build flags 2022-11-24 08:10:13 -06:00
metaeuk biology/metaeuk: Fix build on systems withour OpenMP enabled 2022-12-10 01:51:02 -08:00
migrate
minimap2
mmseqs2
molden
mothur
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit graphics/proj: Update to 9.1.0 2022-11-17 09:20:57 +01:00
ncbi-entrez-direct all: Bump PORTVERSION after lang/go{118,119} update 2023-01-14 06:31:17 -05:00
ncbi-toolkit */*: Bump PORTREVISION for consumers of libunistring 2022-10-22 11:36:07 +02:00
ncbi-vdb
ngs-sdk
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 biology/paml: Update to 4.10.6 2022-11-12 22:35:29 -04:00
pbbam biology/pbbam: Bump PORTREVISION for biology/htslib update 2023-01-05 19:25:09 -06:00
pbseqan
peak-classifier biology/peak-classifier: Update to 0.1.4-5 2022-12-11 14:09:20 -06:00
pear-merger
phrap
phred
phyml
picard-tools
plink
pooler biology/pooler: update to 1.86 2022-12-19 08:56:15 +01:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-bcbio-gff */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-biom-format */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-biopython biology/py-biopython: Update to 1.80 2022-12-05 19:45:16 +08:00
py-biosig biology/py-biosig: New port: Library for reading and writing different biosignal data format 2022-12-30 00:32:02 -08:00
py-bx-python */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-crossmap */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-cutadapt */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-deeptools */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-deeptoolsintervals */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-dna-features-viewer */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-dnaio */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-ete3 */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-Genesis-PyAPI */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-gffutils */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-goatools */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-gtfparse */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-hits */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-libnuml
py-libsedml
py-loompy */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-macs2
py-mrcfile */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-multiqc */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-ont-fast5-api
py-orange3-bioinformatics */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-orange3-single-cell Revert: "all: deprecate ports depending on expired security/py-keyrings.alt" 2022-12-06 12:12:04 +01:00
py-pandas-charm */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-py2bit */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pybigwig */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pyfaidx */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pyrodigal */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pysam */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-PySCeS */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-python-libsbml */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-pywgsim */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-resdk */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-scikit-bio */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-valerius
py-xenaPython */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
pyfasta */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
python-nexus */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
rainbow
rampler
readseq
recombine
rna-seq biology/rna-seq: Update to 0.1.1 2023-01-12 13:02:14 -06:00
ruby-bio Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio-executables Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio-old-biofetch-emulator Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio-shell Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
sam2pairwise
samtools biology/samtools: Update to 1.16.1 2023-01-05 17:17:34 -06:00
scrm
seaview
seqan
seqan1
seqan3
seqan-apps
seqio
seqkit all: Bump PORTVERSION after lang/go{118,119} update 2023-01-14 06:31:17 -05:00
seqtk
sigviewer
sim4
slclust
smithwaterman
snpeff biology/snpeff: Update to 5.1 2022-12-19 12:50:00 -06:00
spoa
sra-tools
stacks
star biology/star: Bump PORTREVISION for biology/htslib update 2023-01-05 19:27:16 -06:00
stringtie
subread
tabixpp biology/tabixpp: Bump PORTREVISION for biology/htslib update 2023-01-05 19:29:30 -06:00
taxonkit all: Bump PORTVERSION after lang/go{118,119} update 2023-01-14 06:31:17 -05:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.11 2022-10-12 12:45:24 +01:00
ucsc-userapps
ugene
unikmer all: Bump PORTVERSION after lang/go{118,119} update 2023-01-14 06:31:17 -05:00
vcf2hap
vcf-split biology/vcf-split: Update to 0.1.5-4 2022-12-11 14:11:33 -06:00
vcflib biology/vcflib: Bump PORTREVISION for biology/htslib update 2023-01-05 19:29:53 -06:00
vcftools
velvet
viennarna
vsearch
vt biology/vt: Bump PORTREVISION for biology/htslib update 2023-01-05 19:19:19 -06:00
wise
Makefile biology/atac-seq: Metaport for ATAC-Seq analysis 2023-01-11 17:47:02 -06:00