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Yuri Victorovich 2ad82a1068 */*: Replace format=bsdtar with format=ustar in tar archive operations 
... because the undocumented format bsdtar adds paxheaders on
some systems, therefore breaking the fetch.

The documentation for format=bsdtar should be added:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=277139

Approved by:	portmgr (blanket unbreak)
2024-02-18 17:48:08 -08:00
..
abyss */*: bump PORTREVISION after the upgrade of MPICH to 4.1.2 2023-12-10 11:23:11 +01:00
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
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 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
barrnap biology/barrnap: Update descr 2022-11-24 19:12:18 -08:00
bbmap Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
bcf-score biology/bcf-score: Unbreak build with clang 16 2023-07-16 08:19:06 -05:00
bcftools biology/bcftools: Update to 1.17 2023-02-24 17:30:58 -06:00
bedtools biology/bedtools: Update to 2.31.1 2023-11-08 10:42:09 -06:00
bfc Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
bifrost biology/bifrost: Update to 1.3.1 2023-11-21 06:58:39 -06:00
bio-mocha biology/bio-mocha: Update to 1.16 2023-01-05 17:21:03 -06:00
bioawk Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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: Update to 0.1.4.13 2023-10-29 17:41:02 -05:00
bioparser biology/bioparser: update 3.0.15 → 3.1.0 2023-08-29 00:32:45 -07:00
biosig */*: bump PORTREVISION after the upgrade to SuiteSparse 2024-01-28 13:02:23 +01:00
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: Temporarily not for non-64-bit architectures 2024-01-11 19:01:51 -08:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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 biology/cytoscape: Broken on armv6, armv7 2022-12-10 23:41:04 -08:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
emboss */*: Refactor with IGNORE_WITH_MYSQL 2023-12-29 19:24:39 +01:00
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
fasda biology/fasda: Update to 0.1.5 2023-10-28 06:32:20 -05:00
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 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 biology/fastp: Update to 0.23.4 2023-05-31 10:40:00 -05:00
fastq-trim biology/fastq-trim: Update to 0.1.3 2023-10-28 06:34:21 -05:00
fastqc biology/fastqc: Update to 0.12.1 2023-03-04 18:17:20 -06:00
fasttree Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
fastx-toolkit biology/fastx-toolkit: Unbreak build on 14-CURRENT 2023-03-07 11:28:13 -06:00
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 biology/freebayes: Drop redundant tabixpp dep 2023-01-22 10:42:34 -06:00
garlic Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
gff2ps biology/gff2ps: drop maintainership 2023-05-21 16:20:36 +00:00
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 accessibility/at-spi2-core: update to 2.46.0 2023-03-02 06:23:10 +01:00
graphlan Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
hmmer all: remove explicit versions in USES=python for "3.x+" 2023-06-27 21:34:34 +02:00
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 all: remove explicit versions in USES=python for "3.x+" 2023-06-27 21:34:34 +02:00
iolib */*: Update WWW to use HTTPS for sourceforge.net projects 2023-11-01 23:11:47 +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: Bump PORTREVISION for biology/htslib update 2023-01-05 19:24:44 -06:00
kallisto biology/kallisto: Update to 0.50.1,1 2023-11-04 08:15:25 -05:00
kmcp all: Bump PORTREVISION after lang/go* update 2024-02-11 10:39:17 +00:00
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 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 all: remove explicit versions in USES=python for "3.x+" 2023-06-27 21:34:34 +02:00
libnuml Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
locarna biology/locarna: Fix build on 14.x and main 2023-12-13 23:11:55 -08:00
mafft */*: Sunset 12.4-RELEASE/12-STABLE from ports tree 2023-12-31 01:37:05 +01:00
mapm3 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
mashmap biology/mashmap: Broken on armv7 2024-01-12 17:57:41 -08:00
megahit biology/megahit: Add cmake patch to respect ports build flags 2022-11-24 08:10:13 -06:00
metaeuk biology/metaeuk: Broken on powerpc64le 2024-02-04 10:27:53 -08:00
migrate MAN[1-5]PREFIX: eleminate its usage and move man to share/man 2024-01-09 16:41:04 +01:00
minimap2 biology/minimap2: Update to 2.25 2023-04-29 09:53:40 -05:00
mmseqs2 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
mummer */*: Update WWW to use HTTPS for sourceforge.net projects 2023-11-06 11:03:47 +01:00
muscle Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
ncbi-blast+ devel/grpc: Update to 1.60.0 2023-12-15 01:03:10 +08:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Broken on armv7 2024-01-20 20:09:20 -08:00
ncbi-entrez-direct all: Bump PORTREVISION after lang/go* update 2024-02-11 10:39:17 +00:00
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 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 biology/p5-Bio-DB-NCBIHelper: Update to 1.7.8 2023-12-25 16:59:52 +08:00
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 biology/p5-BioPerl: Update to 1.007008 2023-10-11 20:57:41 +08:00
p5-BioPerl-Run Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
p5-transdecoder p5-transdecoder: Update to 5.7.1 2023-08-05 15:58:40 -05:00
p5-TrimGalore biology/p5-TrimGalore: Fix build 2023-08-05 22:05:05 +02:00
paml biology/paml: Update to 4.10.7 2023-07-08 00:46:53 -03:00
pbbam biology/pbbam: Bump PORTREVISION for biology/htslib update 2023-01-05 19:25:09 -06:00
pbseqan Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
peak-classifier biology/peak-classifier: Update to 0.1.4.13 2023-10-28 06:38:43 -05:00
pear-merger MANPREFIX: eliminate its usage 2024-01-12 16:11:29 +01:00
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 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: Update to 1.88 2023-09-10 08:06:18 -05:00
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 all: remove explicit versions in USES=python for "3.x+" 2023-06-27 21:34:34 +02:00
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 all: remove explicit versions in USES=python for "3.x+" 2023-06-27 21:34:34 +02:00
py-biosig */*: Update WWW to use HTTPS for sourceforge.net projects 2023-11-06 11:03:47 +01:00
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: Update to 4.6 2024-02-06 06:55:32 -06:00
py-deeptools biology/py-deeptools: Update to 3.5.2 2023-06-19 07:09:17 -05:00
py-deeptoolsintervals */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
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: Update to 1.2.0 2024-02-06 06:51:39 -06:00
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: Peak caller for TF binding sites 2024-01-10 09:19:56 -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 biology/py-orange3-bioinformatics: Change RUN_DEPENDS from py-requests-cache to py-requests-cache0 2023-08-01 00:42:07 +08:00
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 */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
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 3.2.1 → 3.2.2 2024-01-21 01:44:54 -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 */*: rename CHEESESHOP to PYPI in MASTER_SITES 2023-01-11 18:58:34 +03:00
py-resdk biology/py-resdk: relax chardet limitation 2023-12-08 21:55:13 +01:00
py-scikit-bio biology/py-scikit-bio: Update 0.5.8 → 0.5.9 2023-08-03 00:02:05 -07:00
py-valerius biology/py-valerius: New port: Python bioinformatics tools 2022-10-03 21:06:22 -07:00
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 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
rampler *: Bump PORTREVISIONs for math/mpc update to 1.3.1 2023-04-23 09:09:58 +00:00
readseq Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
rna-seq biology/rna-seq: Add biology/star dep to metaport 2023-07-31 09:36:06 -05:00
ruby-bio Mk/**ruby.mk: Switch from USE_RUBY=yes to USES=ruby 2023-01-14 17:08:33 -06:00
rubygem-bio biology/rubygem-bio: Update to 2.0.5 2023-09-30 08:46:30 +08:00
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
salmon devel/onetbb: Update to 2021.11.0 2023-11-28 12:35:02 +01:00
sam2pairwise Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
samtools biology/samtools: Update to 1.17 2023-02-24 17:27:21 -06:00
scrm Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
seaview MANPREFIX: eliminate its usage 2024-01-12 16:11:29 +01:00
seqan Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
seqan-apps biology/seqan-apps: Fix build with llvm16 2023-08-06 23:53:04 +02:00
seqan1 Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
seqan3 biology/seqan3: update 3.2.0 → 3.3.0 2023-09-10 11:10:47 -07:00
seqkit all: Bump PORTREVISION after lang/go* update 2024-02-11 10:39:17 +00:00
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 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 */*: Update WWW to use HTTPS for sourceforge.net projects 2023-11-06 11:03:47 +01:00
spoa biology/spoa: update 4.0.7 → 4.1.0 2023-08-29 09:59:01 -07:00
sra-tools biology/sra-tools: Update to 3.0.6 2023-08-10 12:17:24 -05:00
stacks Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
star biology/star: Fix SIMD issue on non-amd64 2023-08-21 09:33:20 -05:00
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 biology/tabixpp: Deprecate 2023-01-22 11:01:57 -06:00
taxonkit all: Bump PORTREVISION after lang/go* update 2024-02-11 10:39:17 +00:00
treekin */*: chase the upgrade of BLAS / LAPACK to 3.12.0 2024-01-01 12:49:51 +01:00
treepuzzle Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
trimadap biology/trimadap: drop GCC requirement on powerpc64le 2023-08-03 10:40:03 +00:00
trimmomatic Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.11 2022-10-12 12:45:24 +01:00
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 all: Bump PORTREVISION after lang/go* update 2024-02-11 10:39:17 +00:00
vcf-split biology/vcf-split: Update to 0.1.5.10 2023-10-28 06:41:39 -05:00
vcf2hap biology/vcf2hap: Update to 0.1.6.7 2023-10-28 06:44:44 -05:00
vcflib lang/zig: update to 0.11.0 2024-01-01 06:37:19 +01:00
vcftools biology/vcftools: Unbreak build with clang 16 2023-07-15 20:29:00 -05:00
velvet Remove WWW entries moved into port Makefiles 2022-09-07 23:58:51 +02:00
viennarna */*: chase the upgrade of BLAS / LAPACK to 3.12.0 2024-01-01 12:49:51 +01:00
vsearch biology/vsearch: Update to 2.27.0 2024-01-23 07:16:13 -06:00
vt biology/vt: Bump PORTREVISION for biology/htslib update 2023-01-05 19:19:19 -06:00
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