Tobias Kortkamp 310623bb97 *: Clean up some things ... - Fix typos - Remove duplicate variables - Remove nop or unreferenced variables - Add missing ports to the build - Clean up commented PORTREVISION - Add missing USES Reported by: portscan		2021-09-03 15:01:58 +02:00
..
abyss	biology/abyss: Broken on 11	2021-08-21 12:02:36 -07:00
ad2vcf	biology/ad2vcf: Update to 0.1.3.31	2021-08-27 20:28:10 -05:00
artemis
avida
babel
bamtools	biology/bamtools: Update to 2.5.2	2021-07-06 13:10:54 -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
bfc	biology/bfc: Correct sequencing errors from Illumina sequencing data	2021-08-23 12:28:41 -05:00
bioawk
biococoa
biolibc	biology/biolibc: Update to 0.2.0.1	2021-09-02 18:10:21 -05:00
biolibc-tools	biology/biolibc-tools: High-performance tools based on biolibc	2021-08-30 08:09:23 -05:00
bioparser
biosig	biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX	2021-08-16 19:57:30 -07:00
biosoup
biostar-tools	biostar-tools: Update to 1.4.0	2021-08-24 11:46:30 -05:00
bolt-lmm
bowtie
bowtie2	biology/bowtie2: Update to 2.4.4	2021-05-24 11:35:43 -05:00
bwa
canu
cd-hit	biology/cd-hit: fix build on powerpc	2021-06-10 00:35:36 +00:00
cdbfasta
checkm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
clustal-omega
clustalw
cufflinks
cytoscape	biology/cytoscape: mark unconditionally BROKEN	2021-05-12 14:55:52 +03:00
ddocent
diamond	biology/diamond: Update to 2.0.11-1	2021-07-06 10:15:24 -03:00
dsr-pdb
edlib	biology/edlib: Update 1.2.6.20201202 -> 1.2.7	2021-08-21 10:12:15 -07:00
emboss
erminej	biology/erminej: Analyses of gene sets, e.g. gene expression profiling	2021-07-09 07:26:58 -05:00
exonerate
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
fastdnaml
fastool
fastp	biology/fastp: Update to 0.22.0	2021-08-26 14:48:10 -05:00
fastqc
fasttree	biology/fasttree: fix build on armv7	2021-06-15 08:41:19 +00:00
fastx-toolkit
figtree
flash	biology/flash: Fast Length Adjustment of SHort reads	2021-08-23 12:26:47 -05:00
fluctuate
freebayes
garlic
gatk
gcta
gemma	math/gsl: update to 2.7	2021-06-16 21:31:27 +02:00
generand
gff2ps
gmap
gperiodic
graphlan
groopm	math/py-matplotlib: chase minimum Python version in dependent ports	2021-05-10 22:13:20 +02:00
haplohseq
hhsuite	biology/hhsuite: fix build on powerpc64*	2021-07-08 13:13:54 +00:00
hisat2
hmmer
htslib	htslib: Update to 1.13	2021-07-12 08:16:45 -05:00
hyphy	biology/hyphy: Update to 2.4.32	2021-08-20 10:56:52 -03:00
igv	biology/igv: Broken on 11	2021-08-21 12:08:05 -07:00
infernal
iolib	biology/iolib: Drop maintainership	2021-05-19 20:56:24 +01:00
iqtree
jalview	biology/jalview: Fix build	2021-06-27 05:30:39 -04:00
jellyfish	biology/jellyfish: Update to 2.3.0	2021-08-22 12:44:17 -05:00
kallisto
lamarc
libbigwig
libgtextutils
libsbml	biology/libsbml: Rename LIBXML option to LIBXML2	2021-05-12 05:46:56 +08:00
linux-foldingathome	biology/linux-foldingathome: Update to 7.6.21	2021-06-25 19:13:19 +02:00
mafft
mapm3
migrate
minimap2	biology/minimap2: Add pkg-plist to repo	2021-08-22 12:46:37 -05:00
mmseqs2	biology/mmseqs2: Fix runtime error when built with clang	2021-06-29 09:04:48 -05:00
molden	graphics/mesa-libs: Bump reverse deps for libglvnd	2021-06-22 11:53:08 -07:00
mopac
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
muscle
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 22.0.0 -> 25.0.0	2021-08-25 13:28:23 -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
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
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 1.7.7	2021-07-06 22:56:10 +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
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam
pbseqan
peak-classifier	biology/peak-classifier: Update to 0.1.1.21	2021-09-02 18:15:40 -05:00
pear-merger
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
plink
pooler	biology/pooler: Update to 1.78	2021-08-28 09:35:01 -05:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-bigwig	biology/py-bigwig: Fix packaging with Python 3.8+	2021-04-21 09:41:29 +02:00
py-biom-format
py-biopython
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
py-Genesis-PyAPI
py-gffutils
py-goatools	biology/py-goatools: Tools for processing and visualizing Gene Ontology terms	2021-07-02 12:00:29 -05:00
py-gtfparse
py-hits
py-loompy
py-macs2
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
py-pandas-charm
py-pyfaidx	biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5	2021-04-23 14:57:50 -07:00
py-pysam
py-PySCeS	biology/py-PySCeS: New port: Python Simulator for Cellular Systems	2021-08-17 14:30:08 -07:00
py-python-libsbml	biology/py-python-libsbml: New port: LibSBML Python API	2021-08-17 14:30:07 -07:00
py-resdk	biology/py-resdk: Update 13.3.0 -> 13.4.0	2021-08-17 10:29:42 -07:00
py-scikit-bio
py-xenaPython
pyfasta
python-nexus
rainbow
rampler
readseq	biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint	2021-04-18 09:20:28 -05:00
recombine
ruby-bio
rubygem-bio	biology/rubygem-bio: Update to 2.0.2	2021-07-01 04:44:06 +08:00
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
samtools	biology/samtools: Update to 1.13	2021-07-12 08:24:26 -05:00
scrm
seaview	biology/seaview: in preparation to FLTK update, unbreak the port	2021-08-14 08:58:03 +00:00
seqan
seqan1
seqan3	biology/seqan3: Add the 'test' target (currently broken due to lacking clang support)	2021-08-13 10:08:56 -07:00
seqan-apps	biology/seqan-apps: fix packaging on armv7	2021-06-21 08:11:25 +00:00
seqio
seqkit	biology/seqkit: Add 'test' target	2021-08-14 11:53:27 -07:00
seqtk
sigviewer	misc/: Update 0.99.6-2 -> 0.991	2021-08-18 10:17:45 -07:00
sim4
slclust
smithwaterman
snpeff	biology/snpeff: Improvements to Makefile and patches	2021-04-19 11:41:58 -05:00
spoa
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
star
stringtie
subread
tabixpp
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
trimadap
trimmomatic
tRNAscan-SE
ucsc-userapps	biology/ucsc-userapps: Update to v414	2021-05-15 10:23:08 -05:00
ugene	biology/ugene: update Unipro UGENE to version 39.0.	2021-06-25 17:56:47 +00:00
unikmer	*: Clean up some things	2021-09-03 15:01:58 +02:00
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
vcftools
velvet
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
wise
Makefile	biology/biolibc-tools: High-performance tools based on biolibc	2021-08-30 08:09:23 -05:00