:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'etoki' .. highlight: bash etoki ===== .. conda:recipe:: etoki :replaces_section_title: :noindex: EToKi \(Enterobase Tool Kit\) includes methods related to Enterobase data analysis pipelines :homepage: https://github.com/zheminzhou/EToKi :license: GPL3 / GNU General Public v3 (GPLv3) :recipe: /`etoki `_/`meta.yaml `_ .. conda:package:: etoki |downloads_etoki| |docker_etoki| :versions: ``1.2.3-0`` :depends bbmap: :depends blast: :depends bowtie2: :depends bwa: :depends click: :depends curl: :depends diamond: :depends ete3: :depends fasttree: :depends flye: :depends gatk: :depends kraken2: :depends last: :depends megahit: :depends mmseqs2: :depends nextpolish: :depends numba: :depends numpy: ``1.21.6.*`` :depends pandas: :depends perl-lyve-set: :depends piler-cr: :depends pilon: :depends psutil: :depends python: ``>=3.6`` :depends rapidnj: :depends raxml: :depends raxml-ng: :depends samtools: :depends scikit-learn: :depends scipy: :depends simbac: :depends spades: ``>=3.15`` :depends trf: :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 etoki and update with:: mamba update etoki To create a new environment, run:: mamba create --name myenvname etoki 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/etoki: (see `etoki/tags`_ for valid values for ````) .. |downloads_etoki| image:: https://img.shields.io/conda/dn/bioconda/etoki.svg?style=flat :target: https://anaconda.org/bioconda/etoki :alt: (downloads) .. |docker_etoki| image:: https://quay.io/repository/biocontainers/etoki/status :target: https://quay.io/repository/biocontainers/etoki .. _`etoki/tags`: https://quay.io/repository/biocontainers/etoki?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/etoki/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/etoki/README.html