:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'genomics-data-index' .. highlight: bash genomics-data-index =================== .. conda:recipe:: genomics-data-index :replaces_section_title: :noindex: 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 `_ .. conda:package:: genomics-data-index |downloads_genomics-data-index| |docker_genomics-data-index| :versions: ``0.9.2-0`` :depends bamtools: :depends bcftools: ``>=1.13`` :depends bedtools: :depends biocommons.seqrepo: :depends biopython: ``>=1.70`` :depends click: :depends click-config-file: :depends coloredlogs: :depends ete3: :depends fasttree: :depends htslib: ``>=1.13`` :depends iqtree: :depends jinja2: :depends minimap2: :depends numpy: :depends packaging: :depends pandas: ``>=1.0.0`` :depends pathvalidate: :depends pybedtools: :depends pymysql: :depends pyqt: :depends pyroaring: :depends pytest: :depends python: ``>=3.8,<3.10`` :depends pyyaml: :depends requests: :depends requests-html: :depends samtools: ``>=1.13`` :depends scikit-bio: :depends scipy: ``<1.9`` :depends snakemake: :depends snpeff: :depends sourmash: :depends sqlalchemy: :depends vcfpy: :depends zipp: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install genomics-data-index and update with:: mamba update genomics-data-index To create a new environment, run:: mamba create --name myenvname genomics-data-index with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/genomics-data-index: (see `genomics-data-index/tags`_ for valid values for ````) .. |downloads_genomics-data-index| image:: https://img.shields.io/conda/dn/bioconda/genomics-data-index.svg?style=flat :target: https://anaconda.org/bioconda/genomics-data-index :alt: (downloads) .. |docker_genomics-data-index| image:: https://quay.io/repository/biocontainers/genomics-data-index/status :target: https://quay.io/repository/biocontainers/genomics-data-index .. _`genomics-data-index/tags`: https://quay.io/repository/biocontainers/genomics-data-index?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/genomics-data-index/README.html