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ports/biology
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Yuri Victorovich c16b145a0f biology/treekin: Unbreak 
Recent Lapack API changes broke it.

PR:		259179
2021-10-15 08:50:24 -07:00
..
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 py-deeptools to metaport deps
2021-10-14 06:53:52 -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-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: chase ad5a0604c4
2021-10-14 00:53:16 +00:00
py-cutadapt
biology/py-cutadapt: Update strict py-dnaio dep version
2021-05-04 08:20:39 -05:00
py-deeptools
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
2021-10-14 06:51:12 -05:00
py-deeptoolsintervals
biology/py-deeptoolsintervals: Python interface for deepTools interval trees
2021-10-13 11:02:13 -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-bigwig: Rename to biology/py-pybigwig
2021-10-13 16:21:32 -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
biology/treekin: Unbreak
2021-10-15 08:50:24 -07:00
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 40.1 (bugfix release).
2021-10-14 11:23:37 +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-deeptools: User-friendly tools for exploring deep-sequencing data
2021-10-14 06:51:12 -05:00