:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'mlst' .. highlight: bash mlst ==== .. conda:recipe:: mlst :replaces_section_title: :noindex: Scan contig files against PubMLST typing schemes :homepage: https://github.com/tseemann/mlst :license: GPL / GPL-2.0 :recipe: /`mlst `_/`meta.yaml `_ :links: biotools: :biotools:`mlst` .. conda:package:: mlst |downloads_mlst| |docker_mlst| :versions: .. raw:: html
2.23.0-12.23.0-02.22.1-02.22.0-02.19.0-12.19.0-02.18.1-02.18.0-02.17.6-1 ``2.23.0-1``,  ``2.23.0-0``,  ``2.22.1-0``,  ``2.22.0-0``,  ``2.19.0-1``,  ``2.19.0-0``,  ``2.18.1-0``,  ``2.18.0-0``,  ``2.17.6-1``,  ``2.17.6-0``,  ``2.16.4-0``,  ``2.16.2-1``,  ``2.16.2-0``,  ``2.16.1-0``,  ``2.16-0``,  ``2.15.2-0``,  ``2.15.1-0``,  ``2.15-0``,  ``2.14-0``,  ``2.13-0``,  ``2.12-0``,  ``2.11-0``,  ``2.10-1``,  ``2.10-0``,  ``2.9-5``,  ``2.9-4``,  ``2.9-3``,  ``2.9-2``,  ``2.9-1``,  ``2.9-0``,  ``2.6-0`` .. raw:: html
:depends any2fasta: :depends blast: ``>=2.9.0`` :depends curl: :depends parallel: :depends perl: :depends perl-bioperl: ``>=1.7.2`` :depends perl-file-which: :depends perl-json: :depends perl-list-moreutils: :depends perl-lwp-protocol-https: :depends perl-moo: :depends zlib: :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 mlst and update with:: mamba update mlst To create a new environment, run:: mamba create --name myenvname mlst 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/mlst: (see `mlst/tags`_ for valid values for ````) .. |downloads_mlst| image:: https://img.shields.io/conda/dn/bioconda/mlst.svg?style=flat :target: https://anaconda.org/bioconda/mlst :alt: (downloads) .. |docker_mlst| image:: https://quay.io/repository/biocontainers/mlst/status :target: https://quay.io/repository/biocontainers/mlst .. _`mlst/tags`: https://quay.io/repository/biocontainers/mlst?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/mlst/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/mlst/README.html