recipe genomics-data-index

Indexes genomics data (nucleotide variants, kmers, MLST) for fast querying of features.

Homepage:

https://github.com/apetkau/genomics-data-index

License:

Apache-2.0

Recipe:

/genomics-data-index/meta.yaml

package genomics-data-index

Versions:

0.9.2-0

Depends:

• bamtools

• bcftools >=1.13

• bedtools

• biocommons.seqrepo

• biopython >=1.70

• click

• click-config-file

• coloredlogs

• ete3

• fasttree

• htslib >=1.13

• iqtree

• jinja2

• minimap2

• numpy

• packaging

• pandas >=1.0.0

• pathvalidate

• pybedtools

• pymysql

• pyqt

• pyroaring

• pytest

• python >=3.8,<3.10

• pyyaml

• requests

• requests-html

• samtools >=1.13

• scikit-bio

• scipy <1.9

• snakemake

• snpeff

• sourmash

• sqlalchemy

• vcfpy

• zipp

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install genomics-data-index

and update with:

conda update genomics-data-index

or use the docker container:

docker pull quay.io/biocontainers/genomics-data-index:<tag>

(see genomics-data-index/tags for valid values for <tag>)

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/genomics-data-index/README.html)