Jason W. Bacon 904a889fd1 biology/py-pybigwig: Python access to bigWig files using libBigWig ... py-bigwig is a python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. This extension uses libBigWig for local and remote file access.		2021-10-13 08:03:21 -05:00
..
abyss	cleanup: drop support for EOL FreeBSD 11.X	2021-09-30 23:23:30 +02:00
ad2vcf	biology/ad2vcf: Update to 0.1.3.31	2021-08-27 20:28:10 -05:00
artemis	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
avida	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
babel	all: Remove all other $FreeBSD keywords.	2021-04-06 16:31:13 +02:00
bamtools	biology/bamtools: Update to 2.5.2	2021-07-06 13:10:54 -05:00
bamutil	biology/bamutil: Utilities for working with SAM/BAM files	2021-10-12 11:40:35 -05:00
bbmap	biology/bbmap: Update to 38.92	2021-08-22 08:59:58 -05:00
bcftools	biology/bcftools: Update to 1.13	2021-07-12 08:30:10 -05:00
bedtools	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bfc	biology/bfc: Correct sequencing errors from Illumina sequencing data	2021-08-23 12:28:41 -05:00
bioawk	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biococoa	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biolibc	biology/biolibc: Update to 0.2.0.11	2021-09-17 11:33:57 -05:00
biolibc-tools	biology/biolibc-tools: High-performance tools based on biolibc	2021-08-30 08:09:23 -05:00
bioparser	biology/bioparser: Update 3.0.12-2 -> 3.0.15	2021-09-21 09:41:49 -07:00
biosig	biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX	2021-08-16 19:57:30 -07:00
biosoup	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
biostar-tools	biology/biostar-tools: Add biology/bamutil to metaport deps	2021-10-12 11:43:08 -05:00
bolt-lmm	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bowtie	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
bowtie2	biology/bowtie2: Update to 2.4.4	2021-05-24 11:35:43 -05:00
bwa	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
canu	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
cd-hit	biology/cd-hit: fix build on powerpc	2021-06-10 00:35:36 +00:00
cdbfasta	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
checkm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
clustal-omega	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
clustalw	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
cufflinks	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
cytoscape	biology/cytoscape: mark unconditionally BROKEN	2021-05-12 14:55:52 +03:00
ddocent	cleanup: drop support for EOL FreeBSD 11.X	2021-09-30 23:23:30 +02:00
diamond	biology/diamond: Update to 2.0.12	2021-10-12 12:40:55 -03:00
dsr-pdb	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
edlib	biology/edlib: Update 1.2.6.20201202 -> 1.2.7	2021-08-21 10:12:15 -07:00
emboss	biology/emboss: Add "emboss" command in ${LOCALBASE}/bin	2021-09-24 16:34:20 -05:00
erminej	biology/erminej: Analyses of gene sets, e.g. gene expression profiling	2021-07-09 07:26:58 -05:00
exonerate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
fasta	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
fasta3	Deorbit RESTRICTED && NO_CDROM, part one.	2021-05-06 13:47:41 +02:00
fastahack	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fastdnaml	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
fastool	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fastp	biology/fastp: Update to 0.22.0	2021-08-26 14:48:10 -05:00
fastqc	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
fasttree	biology/fasttree: fix build on armv7	2021-06-15 08:41:19 +00:00
fastx-toolkit	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
figtree	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
flash	biology/flash: Fast Length Adjustment of SHort reads	2021-08-23 12:26:47 -05:00
fluctuate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
freebayes	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
garlic	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
gatk	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
gcta	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
gemma	math/gsl: update to 2.7	2021-06-16 21:31:27 +02:00
generand	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
gff2ps	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
gmap	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
gperiodic	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
graphlan	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
groopm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
haplohseq	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
hhsuite	biology/hhsuite: Fix build on aarch64	2021-09-13 17:47:57 +02:00
hisat2	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
hmmer	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
htslib	biology/htslib: Add CPE information	2021-09-10 21:18:20 +00:00
hyphy	biology/hyphy: Enable on aarch64.	2021-10-08 18:27:33 +02:00
igv	cleanup: drop support for EOL FreeBSD 11.X	2021-09-30 23:23:30 +02:00
infernal	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
iolib	biology/iolib: Drop maintainership	2021-05-19 20:56:24 +01:00
iqtree	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
jalview	cleanup: drop support for EOL FreeBSD 11.X	2021-09-30 23:23:30 +02:00
jellyfish	*: Clean up some things	2021-10-12 17:01:38 +02:00
kallisto	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
lamarc	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
libbigwig	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
libgtextutils	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
libneurosim	biology/libneurosim: New port: Common interfaces for neuronal simulators	2021-10-08 10:20:27 -07:00
libnuml	biology/libnuml: New port: C++ library for Numerical Markup Language	2021-09-18 23:47:02 -07:00
libsbml	biology/libsbml: Rename LIBXML option to LIBXML2	2021-05-12 05:46:56 +08:00
libsedml	biology/libsedml: New port: C++ SED-ML library	2021-09-19 11:15:35 -07:00
linux-foldingathome	biology/linux-foldingathome: Update to 7.6.21	2021-06-25 19:13:19 +02:00
mafft	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
mapm3	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
migrate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
minimap2	biology/minimap2: Add pkg-plist to repo	2021-08-22 12:46:37 -05:00
mmseqs2	biology/mmseqs2: disable on 32-bits	2021-09-12 21:05:53 +00:00
molden	graphics/mesa-libs: Bump reverse deps for libglvnd	2021-06-22 11:53:08 -07:00
mopac	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
mothur	biology/mothur: Update 1.46.0 -> 1.46.1	2021-09-02 02:29:56 -07:00
mrbayes	*: Remove unnecessary 'port' argument from USES=readline	2021-05-15 09:14:04 +02:00
mummer	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
muscle	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ncbi-blast+	biology/ncbi-blast+: Update to 2.12.0	2021-07-02 11:48:20 -05:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0	2021-10-01 00:14:37 -07:00
ncbi-entrez-direct	biology/ncbi-entrez-direct: Update to 14.9.20210423_1	2021-04-26 11:53:11 -05:00
ncbi-toolkit	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ncbi-vdb	devel/libepoll-shim: update to 0.0.20210418	2021-04-26 14:17:32 +00:00
ngs-sdk	biology/ngs-sdk: Update 2.11.0-> 2.11.1	2021-08-18 10:17:44 -07:00
p5-AcePerl	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-ASN1-EntrezGene	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Cluster	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Coordinate	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Das	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Das-Lite	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-DB-EMBL	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-DB-NCBIHelper	biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7	2021-07-06 22:56:10 +08:00
p5-Bio-FeatureIO	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-GFF3	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Glite	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Graphics	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-MAGETAB	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-NEXUS	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Phylo	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-SCF	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-Bio-Variation	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-BioPerl	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-BioPerl-Run	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
p5-transdecoder	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
p5-TrimGalore	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
paml	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
pbbam	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
pbseqan	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
peak-classifier	biology/peak-classifier: Update to 0.1.1.21	2021-09-02 18:15:40 -05:00
pear-merger	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
phrap	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
phred	Deorbit RESTRICTED && NO_CDROM, part two.	2021-05-06 13:47:48 +02:00
phyml	Clean up some things	2021-04-15 10:31:56 +02:00
picard-tools	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
plink	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
pooler	biology/pooler: fix build on powerpc	2021-10-06 20:52:30 +00:00
primer3	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
prodigal	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
prodigy-lig	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
protomol	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
psi88	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
py-bigwig	biology/py-bigwig: Fix packaging with Python 3.8+	2021-04-21 09:41:29 +02:00
py-biom-format	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-biopython	biology/py-biopython: Update to 1.79	2021-10-12 14:43:04 +08:00
py-bx-python	biology/py-bx-python: Update 0.8.10 -> 0.8.11-6	2021-08-17 12:10:45 -07:00
py-crossmap	biology/py-crossmap: Update to 0.5.4	2021-04-21 08:31:13 -05:00
py-cutadapt	biology/py-cutadapt: Update strict py-dnaio dep version	2021-05-04 08:20:39 -05:00
py-dnaio	biology/py-dnaio: Update to 0.5.1	2021-05-04 08:19:25 -05:00
py-ete3	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-Genesis-PyAPI	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-gffutils	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-goatools	biology/py-goatools: Tools for processing and visualizing Gene Ontology terms	2021-07-02 12:00:29 -05:00
py-gtfparse	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-hits	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-libnuml	biology/py-libnuml: Fix typo	2021-09-19 11:15:35 -07:00
py-libsedml	biology/py-libsedml: New port: SED-ML library for Python	2021-09-19 11:15:36 -07:00
py-loompy	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-macs2	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-multiqc	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
py-ont-fast5-api	biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files	2021-08-13 08:34:09 -05:00
py-orange3-bioinformatics	biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1	2021-04-27 01:56:19 -07:00
py-orange3-single-cell	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-pandas-charm	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-py2bit	biology/py-py2bit: Python interface for 2bit packed nucleotide files	2021-10-13 07:53:53 -05:00
py-pybigwig	biology/py-pybigwig: Python access to bigWig files using libBigWig	2021-10-13 08:03:21 -05:00
py-pyfaidx	biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5	2021-04-23 14:57:50 -07:00
py-pysam	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-PySCeS	biology/py-PySCeS: Update 0.9.8a -> 1.0.0	2021-09-20 14:34:22 -07:00
py-python-libsbml	biology/py-python-libsbml: New port: LibSBML Python API	2021-08-17 14:30:07 -07:00
py-pywgsim	biology/py-pywgsim: Modified wgsim genomic data simulator	2021-09-06 07:55:49 -05:00
py-resdk	biology/py-resdk: Update 13.3.0 -> 13.4.0	2021-08-17 10:29:42 -07:00
py-scikit-bio	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
py-xenaPython	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
pyfasta	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
python-nexus	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rainbow	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
rampler	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
readseq	biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint	2021-04-18 09:20:28 -05:00
recombine	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ruby-bio	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio	biology/rubygem-bio: Update to 2.0.2	2021-07-01 04:44:06 +08:00
rubygem-bio-executables	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio-old-biofetch-emulator	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
rubygem-bio-shell	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
sam2pairwise	biology/sam2pairwise: Show pairwise alignment for each read in a SAM file	2021-09-07 15:32:29 -05:00
samtools	biology/samtools: Update to 1.13	2021-07-12 08:24:26 -05:00
scrm	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
seaview	biology/seaview: in preparation to FLTK update, unbreak the port	2021-08-14 08:58:03 +00:00
seqan	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqan1	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqan3	biology/seqan3: Add the 'test' target (currently broken due to lacking clang support)	2021-08-13 10:08:56 -07:00
seqan-apps	*/*: Remove compiler:openmp from Mk/Uses/compiler.mk	2021-10-03 19:47:27 +02:00
seqio	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
seqkit	biology/seqkit: Update 0.16.1 -> 2.0.1	2021-09-18 10:48:26 -07:00
seqtk	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
sigviewer	misc/: Update 0.99.6-2 -> 0.991	2021-08-18 10:17:45 -07:00
sim4	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
slclust	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
smithwaterman	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
snpeff	biology/snpeff: Improvements to Makefile and patches	2021-04-19 11:41:58 -05:00
spoa	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
sra-tools	biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives	2021-06-22 12:55:15 -05:00
stacks	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
star	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
stringtie	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
subread	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
tabixpp	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
taxonkit	biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit	2021-05-26 15:25:22 -07:00
treekin	math/lapack: +math/blas et al., upgrade to 3.9.1	2021-06-13 19:48:12 +02:00
treepuzzle	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
trimadap	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
trimmomatic	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
tRNAscan-SE	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
ucsc-userapps	biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin	2021-09-24 16:53:30 -05:00
ugene	biology/ugene: update Unipro UGENE to version 40.0.	2021-09-16 09:48:26 +00:00
unikmer	biology/unikmer: Update 0.18.4 -> 0.18.8	2021-09-26 01:54:07 -07:00
vcf2hap	biology/vcf2hap: Update to 0.1.3.12	2021-08-27 20:32:51 -05:00
vcf-split	biology/vcf-split: Update to 0.1.2.14	2021-08-27 20:30:52 -05:00
vcflib	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
vcftools	biology/vcftools: Add CPE information	2021-09-25 20:28:38 +00:00
velvet	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
viennarna	math/gsl: update to 2.7	2021-06-16 21:31:27 +02:00
vsearch	biology/vsearch: Update to 2.17.1	2021-06-19 07:33:58 -05:00
vt	One more small cleanup, forgotten yesterday.	2021-04-07 10:09:01 +02:00
wise	Remove # $FreeBSD$ from Makefiles.	2021-04-06 16:31:07 +02:00
Makefile	biology/py-pybigwig: Python access to bigWig files using libBigWig	2021-10-13 08:03:21 -05:00