:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'rnaquast' .. highlight: bash rnaquast ======== .. conda:recipe:: rnaquast :replaces_section_title: :noindex: rnaQUAST is a tool for evaluating RNA\-Seq assemblies using reference genome and gene database. In addition\, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third\-party software. :homepage: http://cab.spbu.ru/software/rnaquast/ :license: GPLv2 :recipe: /`rnaquast `_/`meta.yaml `_ .. conda:package:: rnaquast |downloads_rnaquast| |docker_rnaquast| :versions: .. raw:: html
2.2.3-02.2.1-02.2.0-22.2.0-12.2.0-02.1.0-12.1.0-02.0.1-02.0.0-0 ``2.2.3-0``,  ``2.2.1-0``,  ``2.2.0-2``,  ``2.2.0-1``,  ``2.2.0-0``,  ``2.1.0-1``,  ``2.1.0-0``,  ``2.0.1-0``,  ``2.0.0-0``,  ``1.5.1-0`` .. raw:: html
:depends blast: :depends blat: :depends busco: ``>=5`` :depends emboss: :depends gffutils: :depends gmap: ``<2021.02.22,>=2020.03.12`` :depends joblib: :depends matplotlib-base: :depends python: :depends samtools: :depends star: :depends ucsc-pslsort: :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 rnaquast and update with:: mamba update rnaquast To create a new environment, run:: mamba create --name myenvname rnaquast 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/rnaquast: (see `rnaquast/tags`_ for valid values for ````) .. |downloads_rnaquast| image:: https://img.shields.io/conda/dn/bioconda/rnaquast.svg?style=flat :target: https://anaconda.org/bioconda/rnaquast :alt: (downloads) .. |docker_rnaquast| image:: https://quay.io/repository/biocontainers/rnaquast/status :target: https://quay.io/repository/biocontainers/rnaquast .. _`rnaquast/tags`: https://quay.io/repository/biocontainers/rnaquast?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/rnaquast/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/rnaquast/README.html