Mathieu Arnold 0660187ad0 cleanup: remove occurrences of WITH_DEBUG ... DEBUG like all ports features, must not ever be set in a port, they are user facing features, that the user needs to enable in their environment/make.conf, either by defining WITH_DEBUG globally, or by setting WITH_DEBUG_PORTS with origin of ports they want DEBUG enabled in.		2024-04-12 08:04:05 +02:00
..
abyss	biology/abyss: Move man pages to share/man	2024-03-03 10:04:08 +00:00
ad2vcf	biology/ad2vcf: Move man pages to share/man	2024-03-02 18:32:34 +00:00
artemis
atac-seq	biology/atac-seq: Update to 0.2.0	2024-01-10 10:05:41 -06:00
augustus	*/*: bump PORTREVISION after the upgrade to SuiteSparse	2024-01-28 13:02:23 +01:00
avida	*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree	2023-12-31 01:37:05 +01:00
babel	biology/babel: Update WWW	2023-10-30 23:37:03 +01:00
bamtools
bamutil
barrnap
bbmap
bcf-score	biology/bcf-score: Unbreak build with clang 16	2023-07-16 08:19:06 -05:00
bcftools	biology/bcftools: Move man pages to share/man	2024-03-02 18:38:43 +00:00
bedtools	biology/bedtools: Update to 2.31.1	2023-11-08 10:42:09 -06:00
bfc
bifrost	biology/bifrost: Update to 1.3.5	2024-03-18 09:29:43 -05:00
bio-mocha
bioawk
biococoa	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
biolibc	biology/biolibc: Impelled to share/man	2024-01-23 15:51:25 +01:00
biolibc-tools	biology/biolibc-tools: Move man pages to share/man	2024-03-02 18:44:44 +00:00
bioparser	biology/bioparser: update 3.0.15 → 3.1.0	2023-08-29 00:32:45 -07:00
biosig	biology/{,py-}biosig: update 2.5.2 → 2.6.0	2024-04-05 18:04:45 -07:00
biosoup	biology/biosoup: Install cmake files	2023-08-29 00:32:45 -07:00
biostar-tools	biology/biostar-tools: Update to 1.10.1_3	2024-02-16 07:42:11 -06:00
bolt-lmm	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
bowtie	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
bowtie2	biology/bowtie2: Update to 2.5.3	2024-01-18 17:20:08 -06:00
btllib	biology/btllib: update 1.7.1 → 1.7.2	2024-04-09 00:40:58 -07:00
bwa	MAN?PREFIX: eleminate its usage and move man to share/man	2024-01-10 09:16:01 +01:00
canu	biology/canu: Fix build with llvm16	2023-07-20 19:42:34 +02:00
cd-hit	biology/cd-hit: allow to build without GCC on libomp-less systems	2023-08-12 03:37:47 +02:00
cdbfasta	biology/cdbfasta: Update to 2023.07.10	2023-07-11 10:40:27 -05:00
checkm	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
chip-seq	biology/chip-seq: Metaport for ChIP-Seq analysis	2023-06-14 16:23:37 -05:00
clustal-omega
clustalw	biology/clustalw: Unbreak build for clang 16	2023-07-15 18:18:42 -05:00
cufflinks	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
cytoscape
ddocent	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
diamond	biology/diamond: Update to 2.1.9	2024-02-04 15:41:51 -04:00
dsr-pdb	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
edlib
emboss	*/*: Refactor with IGNORE_WITH_MYSQL	2023-12-29 19:24:39 +01:00
erminej
exonerate	biology/exonerate: Moved man to share/man	2024-02-22 14:23:45 +01:00
fasda	biology/fasda: Move man pages to share/man	2024-03-02 19:03:05 +00:00
fasta	MAN[1-5]PREFIX: eleminate its usage and move man to share/man	2024-01-09 16:41:04 +01:00
fasta3	MAN?PREFIX: eleminate its usage and move man to share/man	2024-01-10 09:16:01 +01:00
fastahack
fastdnaml
fastool
fastp	biology/fastp: Update to 0.23.4	2023-05-31 10:40:00 -05:00
fastq-trim	biology/fastq-trim: Move man pages to share/man	2024-03-02 19:08:45 +00:00
fastqc	biology/fastqc: Update to 0.12.1	2023-03-04 18:17:20 -06:00
fasttree
fastx-toolkit	biology/fastx-toolkit: Unbreak build on 14-CURRENT	2023-03-07 11:28:13 -06:00
figtree
flash
fluctuate
freebayes
garlic
gatk	*/*: Replace format=bsdtar with format=ustar in tar archive operations	2024-02-18 17:48:08 -08:00
gcta	biology/gcta: chase the upgrade of OpenBLAS	2023-12-12 20:03:50 +01:00
gemma	*/*: bump PORTREVISION after the upgrade of OpenBLAS	2023-12-12 20:03:50 +01:00
generand	biology/generand: Move man pages to share/man	2024-03-02 19:14:06 +00:00
gff2ps	biology/gff2ps: drop maintainership	2023-05-21 16:20:36 +00:00
gffread
gmap
gperiodic	accessibility/at-spi2-core: update to 2.46.0	2023-03-02 06:23:10 +01:00
graphlan
groopm	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
haplohseq	devel/boost: bump consumers after library update	2024-02-13 17:44:22 +03:00
hhsuite	*/*: bump PORTREVISION after OpenMPI upgrade	2024-02-18 10:29:31 +01:00
hisat2
hmmer	biology/hmmer: Moved man to share/man	2024-02-22 14:23:46 +01:00
htslib	biology/htslib: Moved man to share/man	2024-01-27 13:37:30 +01:00
hyphy	biology/hyphy: Update to 2.5.58	2023-12-23 13:28:25 -04:00
igv	audio/opus: bump consumers after update to 1.4	2023-04-25 17:17:15 +02:00
infernal	biology/infernal: Moved man to share/man	2024-02-22 14:23:47 +01:00
iolib	biology/iolib: Moved man to share/man	2024-02-22 14:23:48 +01:00
iqtree	biology/iqtree: Update to 2.2.2.7	2023-09-04 23:45:37 -03:00
jalview	biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1	2023-06-18 02:58:53 -07:00
jellyfish	biology/jellyfish: Move man pages to share/man	2024-03-02 19:17:36 +00:00
kallisto	biology/kallisto: Update to 0.50.1,1	2023-11-04 08:15:25 -05:00
kmcp	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
lamarc	biology/lamarc: Mark BROKEN on 14	2023-08-18 08:57:13 +02:00
libbigwig	biology/libbigwig: Fix name-clashing in roundup	2023-12-28 18:03:34 -05:00
libcombine	biology/libcombine: Fix build with libsbml 5.20.0	2023-05-27 12:24:05 +08:00
libgff
libgtextutils
libneurosim	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
libnuml
libsbml	biology/libsbml: Update to 5.20.2	2023-09-30 08:44:19 +08:00
libsedml	biology/libsedml: Fix build with libsbml 5.20.0	2023-05-27 12:24:05 +08:00
linux-foldingathome
locarna	biology/locarna: Move man pages to share/man	2024-03-03 10:04:08 +00:00
mafft	biology/mafft: Moved man to share/man	2024-02-22 14:23:49 +01:00
mapm3
mashmap	biology/mashmap: Broken on armv7	2024-01-12 17:57:41 -08:00
megahit
metaeuk	biology/metaeuk: Broken on powerpc64le	2024-02-04 10:27:53 -08:00
migrate	biology/migrate: Fix distinfo	2024-04-09 08:29:35 +01:00
minimap2	biology/minimap2: Update to 2.28	2024-04-10 07:28:02 -05:00
mmseqs2
molden	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
mothur	biology/mothur: Remove CC/CPP/CXX exports	2023-09-28 20:56:25 +02:00
mrbayes
mummer	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
muscle
ncbi-blast+	devel/grpc: Update to 1.62.0	2024-03-09 22:05:20 +08:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: update 28.0.2 → 28.0.3	2024-04-03 09:50:30 -07:00
ncbi-entrez-direct	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
ncbi-toolkit	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
ncbi-vdb	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
ngs-sdk	biology/ngs-sdk: Not for powerpc, powerpc64le	2024-02-02 13:33:37 -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	biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8	2023-12-25 16:59:52 +08:00
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	biology/p5-BioPerl: Update to 1.007008	2023-10-11 20:57:41 +08:00
p5-BioPerl-Run
p5-transdecoder	p5-transdecoder: Update to 5.7.1	2023-08-05 15:58:40 -05:00
p5-TrimGalore	biology/p5-TrimGalore: Release to ports@	2024-04-05 19:12:17 -05:00
paml	biology/paml: Update to 4.10.7	2023-07-08 00:46:53 -03:00
pbbam
pbseqan	biology/pbseqan: Set EXPIRATION_DATE	2024-04-04 18:35:51 +02:00
peak-classifier	biology/peak-classifier: Clean up USES=python	2024-04-05 08:43:40 +08:00
pear-merger	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
phrap
phred
phyml	biology/phyml: fix build on non-x86	2023-05-08 10:25:50 +02:00
picard-tools	*/*: Refactor java/openjdk7 removal	2023-04-04 13:10:53 -05:00
plink	*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree	2023-12-31 01:37:05 +01:00
pooler	biology/pooler: Moved man to share/man	2024-02-22 14:23:50 +01:00
primer3	biology/primer3: Fix build with llvm16	2023-08-05 20:55:50 +02:00
prodigal	biology/prodigal: Update 2.6.3-7 → 2.6.3-16	2023-07-22 00:37:33 -07:00
prodigy-lig	biology/prodigy-lig: update 1.0.1 → 1.1.0	2024-03-21 03:08:33 -07:00
protomol	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-01 23:11:47 +01:00
psi88	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-bcbio-gff	biology/py-bcbio-gff: Update to 0.7.0	2023-03-16 17:32:06 -05:00
py-biom-format	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-biopython	biology/py-biopython: Update to 1.83	2024-04-08 02:29:37 +00:00
py-biosig	biology/{,py-}biosig: update 2.5.2 → 2.6.0	2024-04-05 18:04:45 -07:00
py-bx-python	biology/py-bx-python: update 0.10.0 → 0.11.0	2024-02-12 15:07:35 -08:00
py-crossmap	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-cutadapt	biology/py-cutadapt: Release to ports@	2024-04-05 19:12:16 -05:00
py-deeptools	biology/py-deeptools: Update to 3.5.2	2023-06-19 07:09:17 -05:00
py-deeptoolsintervals
py-dna-features-viewer	biology/py-dna-features-viewer: Update to 3.1.3	2023-11-04 17:11:34 -05:00
py-dnaio	biology/py-dnaio: Release to ports@	2024-04-10 18:41:31 -05:00
py-ete3	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-Genesis-PyAPI	biology/py-Genesis-PyAPI: Add NO_ARCH	2023-08-01 00:42:07 +08:00
py-gffutils	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-goatools	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-gtfparse	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-hits	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-htseq	biology/py-htseq: Fix build with python-3.11	2024-01-21 07:13:35 +00:00
py-libnuml	biology/py-libnuml: Allow build with swig 4.1.0+	2023-04-19 02:05:12 +08:00
py-libsedml	biology/py-libsedml: Allow build with swig 4.1.0+	2023-04-19 02:05:12 +08:00
py-loompy	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-macs2	biology/py-macs2: Update to 2.2.9.1	2023-08-06 13:17:52 -05:00
py-macs3	biology/py-macs3: Update to 3.0.1	2024-02-28 07:29:15 -06:00
py-mrcfile	biology/py-mrcfile: update 1.4.3 → 1.5.0	2024-01-19 23:47:54 -08:00
py-multiqc	biology/py-multiqc: Update to 1.15	2023-08-05 11:18:37 -05:00
py-newick	biology/py-newick: Add new port	2024-02-03 00:58:29 +00:00
py-ont-fast5-api	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
py-orange3-bioinformatics	devel/py-setuptools-scm: update to 8.0.4	2024-02-29 02:18:32 -05:00
py-orange3-single-cell	biology/py-orange3-single-cell: Add NO_ARCH	2023-08-01 00:42:07 +08:00
py-pandas-charm	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-py2bit
py-pybigwig	biology/py-pybigwig: Update to 0.3.22	2023-12-16 07:59:37 -06:00
py-pyfaidx	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
py-pyrodigal	biology/py-pyrodigal: update 3.2.2 → 3.3.0	2024-03-08 14:34:40 -08:00
py-pysam	biology/py-pysam: relax python version requirement	2023-12-03 14:51:05 +03:00
py-PySCeS	biology/py-PySCeS: Fix build by adding USES=localbase:ldflags	2023-12-14 00:43:06 -08:00
py-python-libsbml	biology/py-python-libsbml: relax python version requirement	2023-12-03 15:02:23 +03:00
py-pywgsim
py-resdk	biology/py-resdk: update 20.0.0 → 21.1.0	2024-04-05 18:04:45 -07:00
py-scikit-bio	biology/py-scikit-bio: update 0.5.9 → 0.6.0	2024-04-05 18:04:46 -07:00
py-valerius
py-xenaPython	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
pyfasta	all: remove explicit versions in USES=python for "3.x+"	2023-06-27 21:34:34 +02:00
python-nexus	biology/python-nexus: Update to 2.9.0 and fix build with python-3.11	2024-02-03 00:58:29 +00:00
R-cran-Biobase	biology/R-cran-Biobase: New port	2023-12-15 13:55:44 +01:00
R-cran-BiocGenerics	biology/R-cran-BiocGenerics: New port	2023-12-15 13:55:44 +01:00
R-cran-BiocManager	biology/R-cran-BiocManager: New port	2023-12-15 13:55:43 +01:00
rainbow
rampler	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
readseq
rna-seq	biology/rna-seq: Add biology/star dep to metaport	2023-07-31 09:36:06 -05:00
ruby-bio
rubygem-bio	biology/rubygem-bio: Update to 2.0.5	2023-09-30 08:46:30 +08:00
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
salmon	cleanup: remove occurrences of WITH_DEBUG	2024-04-12 08:04:05 +02:00
sam2pairwise
samtools	biology/samtools: Move man pages to share/man	2024-03-02 19:40:58 +00:00
scrm	biology/scrm: Move man pages to share/man	2024-03-02 19:59:23 +00:00
seaview	MANPREFIX: eliminate its usage	2024-01-12 16:11:29 +01:00
seqan
seqan1
seqan3	biology/seqan3: update 3.2.0 → 3.3.0	2023-09-10 11:10:47 -07:00
seqan-apps	biology/seqan-apps: Fix build with llvm16	2023-08-06 23:53:04 +02:00
seqkit	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
seqtk	biology/seqtk: Update to 1.4	2023-05-23 17:42:13 -05:00
seqwish	biology/seqwish: Add comment	2023-11-05 15:07:52 -08:00
sigviewer	*: Bump PORTREVISIONs for math/mpc update to 1.3.1	2023-04-23 09:09:58 +00:00
slclust
smithwaterman
snpeff	*/*: Update WWW to use HTTPS for sourceforge.net projects	2023-11-06 11:03:47 +01:00
spoa	biology/spoa: Broken on i386	2024-04-11 21:05:12 -07:00
sra-tools	cleanup: remove occurrences of WITH_DEBUG	2024-04-12 08:04:05 +02:00
stacks
star	biology/star: Fix SIMD issue on non-amd64	2023-08-21 09:33:20 -05:00
stringtie
subread
tabixpp
taxonkit	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
treekin	biology/treekin: Move man pages to share/man	2024-03-02 20:02:27 +00:00
treepuzzle
trimadap	biology/trimadap: drop GCC requirement on powerpc64le	2023-08-03 10:40:03 +00:00
trimmomatic	biology/trimmomatic: Release to ports@	2024-04-05 19:12:17 -05:00
tRNAscan-SE
ucsc-userapps	biology/ucsc-userapps: Replace dependencies	2023-12-30 08:16:41 +01:00
ugene	MAN?PREFIX: eleminate its usage and move man to share/man	2024-01-10 09:16:01 +01:00
unikmer	lang/go: Change DEFAULT to 1.21	2024-03-24 15:29:00 +01:00
vcf2hap	biology/vcf2hap: Move man pages to share/man	2024-03-02 20:07:47 +00:00
vcf-split	biology/vcf-split: Move man pages to share/man	2024-03-02 20:04:57 +00:00
vcflib	biology/vcflib: Move man pages to share/man	2024-03-02 20:35:56 +00:00
vcftools	biology/vcftools: Move man pages to share/man	2024-03-02 20:35:56 +00:00
velvet
viennarna	biology/viennarna: Move man pages to share/man	2024-03-02 20:35:56 +00:00
vsearch	biology/vsearch: Update to 2.27.1	2024-04-08 16:43:20 -05:00
vt
wfa2-lib	biology/wfa2-lib: Update to 2.3.4	2023-09-29 13:24:07 -05:00
wise	*/*: Fix build with llvm16 on 13.2-STABLE	2023-07-26 02:48:20 +02:00
Makefile	biology/py-newick: Add new port	2024-02-03 00:58:29 +00:00