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freebsd-ports/biology
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Dmitry Marakasov 463cdea856 biology/cytoscape: mark unconditionally BROKEN 
Approved by:	portmgr blanket
2021-05-12 14:55:52 +03:00
..
abyss
biology/abyss: Update 2.3.0-3 -> 2.3.1
2021-04-22 10:18:02 -07:00
ad2vcf
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
bbmap
biology/bbmap: BBMap short read aligner, and other bioinformatic tools
2021-04-18 11:21:29 -05:00
bcftools
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
bedtools
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
bioparser
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
biosoup
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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: Add support for powerpc64le
2021-04-18 10:53:14 -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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
diamond
biology/diamond: Update to 2.0.9
2021-04-12 21:55:49 -03:00
dsr-pdb
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
edlib
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
emboss
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fastqc
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
fasttree
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +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
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
hyphy
biology/hyphy: Update to 2.5.30
2021-04-07 22:54:50 -03:00
igv
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
infernal
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
iolib
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
iqtree
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
jalview
Clean up some things
2021-05-01 19:55:55 +02:00
jellyfish
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +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
libsbml
biology/libsbml: Rename LIBXML option to LIBXML2
2021-05-12 05:46:56 +08:00
linux-foldingathome
Deorbit RESTRICTED && NO_CDROM, part one.
2021-05-06 13:47:41 +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: Update to 2.18
2021-04-11 14:18:02 -05:00
molden
Deorbit RESTRICTED && NO_CDROM, part one.
2021-05-06 13:47:41 +02:00
mopac
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
mothur
biology/mothur: Update 1.45.2 -> 1.45.3
2021-05-09 09:11:11 -07:00
mrbayes
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +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+
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
ncbi-cxx-toolkit
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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: Fix build on non-amd64 architectures that was broken by explicit 'amd64' instead of $ARCH
2021-04-15 10:01:31 -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
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
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
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
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
py-bx-python
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
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-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-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-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-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-resdk
biology/py-resdk: Update 13.1.0 -> 13.2.0
2021-05-05 12:56:26 -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
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
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
samtools
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
scrm
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
seaview
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
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: Correct dependencies
2021-05-11 22:46:21 -07:00
seqan-apps
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
seqio
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
seqkit
biology/seqkit: Change WWW to the project URL (from GitHub URL)
2021-04-16 21:00:56 -07:00
seqtk
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
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
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
treekin
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +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
Deorbit RESTRICTED && NO_CDROM, part one.
2021-05-06 13:47:41 +02:00
ugene
biology/ugene: mark BROKEN (does not fetch)
2021-05-12 14:55:32 +03:00
vcf2hap
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
vcf-split
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
vcflib
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
vcftools
One more small cleanup, forgotten yesterday.
2021-04-07 10:09:01 +02:00
velvet
Remove # $FreeBSD$ from Makefiles.
2021-04-06 16:31:07 +02:00
viennarna
biology/viennarna: Update 2.4.17 -> 2.4.18
2021-04-23 18:57:38 -07:00
vsearch
biology/vsearch: Update to 2.17.0
2021-04-10 09:02:55 -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
New port: biology/seqan3: C++ header-only library for biological sequence analysis
2021-05-11 18:21:38 -07:00