Package Recipe 'genomics-data-index'

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:

on bamtools
on bcftools >=1.13
on bedtools
on biocommons.seqrepo
on biopython >=1.70
on click
on click-config-file
on coloredlogs
on ete3
on fasttree
on htslib >=1.13
on iqtree
on jinja2
on minimap2
on numpy
on packaging
on pandas >=1.0.0
on pathvalidate
on pybedtools
on pymysql
on pyqt
on pyroaring
on pytest
on python >=3.8,<3.10
on pyyaml
on requests
on requests-html
on samtools >=1.13
on scikit-bio
on scipy <1.9
on snakemake
on snpeff
on sourmash
on sqlalchemy
on vcfpy
on zipp

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install genomics-data-index

to add into an existing workspace instead, run:

pixi add genomics-data-index

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install genomics-data-index

Alternatively, to install into a new environment, run:

conda create -n envname genomics-data-index

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)