mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2024-12-20 04:02:27 +00:00
Code Issues Releases Activity
f1c1dfad23
freebsd-ports/biology
History
Jason W. Bacon 5a2a6eb329 biology/peak-classifier: Classify peaks based on GFF features 
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons.  This is the default for
common data sources.
2021-06-14 11:40:33 -05:00
..
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 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 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 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 biology/fasttree: fix build on powerpc 2021-06-10 12:25:31 +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 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 2.5.31 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 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 2.20 2021-05-29 16:06:34 -05:00
molden Deorbit RESTRICTED && NO_CDROM, part one. 2021-05-06 13:47:41 +02:00
mopac 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 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+ 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
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 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 13.2.0 -> 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 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: Update 3.0.2-1195 -> 3.0.3 2021-05-29 22:38:08 -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: 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 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
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: 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 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 biology/peak-classifier: Classify peaks based on GFF features 2021-06-14 11:40:33 -05:00