:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'mgca' .. highlight: bash mgca ==== .. conda:recipe:: mgca :replaces_section_title: :noindex: Microbial genome component and annotation pipeline :homepage: https://github.com/liaochenlanruo/mgca/blob/master/README.md :documentation: https://liaochenlanruo.fun/mgca/ :developer docs: https://github.com/liaochenlanruo/mgca/tree/master :license: GPL / GPLv3 :recipe: /`mgca `_/`meta.yaml `_ :links: biotools: :biotools:`mgca` Microbial genome component and annotation pipeline. .. conda:package:: mgca |downloads_mgca| |docker_mgca| :versions: ``0.0.0-0`` :depends bakta: ``1.4.0.*`` :depends eggnog-mapper: ``2.1.7.*`` :depends emboss: :depends islandpath: ``1.0.6.*`` :depends lastz: ``1.04.15.*`` :depends mummer4: ``4.0.0rc1.*`` :depends opfi: ``0.1.2.*`` :depends perl: ``>=5.32.1,<6.0a0 *_perl5`` :depends perl-bioperl: :depends phispy: ``4.2.21.*`` :depends r-ggplot2: :depends repeatmasker: ``4.1.2.p1.*`` :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 mgca and update with:: mamba update mgca To create a new environment, run:: mamba create --name myenvname mgca 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/mgca: (see `mgca/tags`_ for valid values for ````) .. |downloads_mgca| image:: https://img.shields.io/conda/dn/bioconda/mgca.svg?style=flat :target: https://anaconda.org/bioconda/mgca :alt: (downloads) .. |docker_mgca| image:: https://quay.io/repository/biocontainers/mgca/status :target: https://quay.io/repository/biocontainers/mgca .. _`mgca/tags`: https://quay.io/repository/biocontainers/mgca?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/mgca/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/mgca/README.html