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freebsd-ports/biology
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Piotr Kubaj 5240cba243 biology/fasttree: fix build on armv7 
Same issue as with powerpc.
2021-06-15 08:41:19 +00:00
..
abyss biology/abyss: Update 2.3.0-3 -> 2.3.1 2021-04-22 10:18:02 -07:00
ad2vcf biology/ad2vcf: Remove comment used to silence portlint 2021-06-11 10:39:02 -05:00
artemis
avida
babel
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
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 biology/biolibc: Remove comment used to silence portlint 2021-06-11 10:38:27 -05:00
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: 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
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
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
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 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastdnaml
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 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
fluctuate
freebayes One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
garlic
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
gmap
gperiodic
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
htslib
hyphy biology/hyphy: Update to 2.5.31 2021-06-05 20:00:24 -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 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 biology/jalview: Broken on 11 2021-06-05 11:53:07 -07:00
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
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
mapm3
migrate
minimap2 biology/minimap2: Update to 2.20 2021-05-29 16:06:34 -05:00
molden Deorbit RESTRICTED && NO_CDROM, part one. 2021-05-06 13:47:41 +02:00
mopac
mothur biology/mothur: Update 1.45.2 -> 1.45.3 2021-05-09 09:11:11 -07:00
mrbayes *: Remove unnecessary 'port' argument from USES=readline 2021-05-15 09:14:04 +02:00
mummer
muscle
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
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
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
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 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
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: Classify peaks based on GFF features 2021-06-14 11:40:33 -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 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
primer3
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
psi88
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
py-bx-python
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 13.2.0 -> 13.3.0 2021-05-24 00:26:50 -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
python-nexus
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
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
samtools
scrm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
seaview
seqan
seqan1
seqan3 biology/seqan3: Update 3.0.2-1195 -> 3.0.3 2021-05-29 22:38:08 -07:00
seqan-apps
seqio
seqkit biology/seqkit: Update 0.16.0 -> 0.16.1 2021-05-19 23:02:26 -07:00
seqtk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
sim4
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
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 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
trimmomatic
tRNAscan-SE
ucsc-userapps biology/ucsc-userapps: Update to v414 2021-05-15 10:23:08 -05:00
ugene - Update Unipro UGENE to version 38.1 and thus unbreak 2021-05-18 15:24:55 +00:00
unikmer biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set operations on k-mers 2021-05-26 15:25:21 -07:00
vcf2hap biology/vcf2hap: Remove comment used to silence portlint 2021-06-11 10:40:11 -05:00
vcf-split biology/vcf-split: Update to 0.1.2 2021-06-11 10:05:19 -05:00
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
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
Makefile biology/peak-classifier: Classify peaks based on GFF features 2021-06-14 11:40:33 -05:00