:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'smeg' .. highlight: bash smeg ==== .. conda:recipe:: smeg :replaces_section_title: :noindex: Strain\-level Metagenomic Estimation of Growth rate \(SMEG\) measures growth rates of microbial strains from complex metagenomic dataset :homepage: https://github.com/ohlab/SMEG :license: MIT :recipe: /`smeg `_/`meta.yaml `_ .. conda:package:: smeg |downloads_smeg| |docker_smeg| :versions: .. raw:: html
1.1.5-21.1.5-11.1.5-01.1.4-11.1.4-01.1.3-01.1.2-01.1.1-01.1-1 ``1.1.5-2``,  ``1.1.5-1``,  ``1.1.5-0``,  ``1.1.4-1``,  ``1.1.4-0``,  ``1.1.3-0``,  ``1.1.2-0``,  ``1.1.1-0``,  ``1.1-1``,  ``1.1-0``,  ``1.0.1-2``,  ``1.0.1-1``,  ``1.0.1-0`` .. raw:: html
:depends bamtools: :depends bedtools: :depends blast: :depends bowtie2: :depends libgenome: :depends mauve: :depends openssl: ``>=1.1.0,<=1.1.1`` :depends parallel: :depends prokka: :depends r-ape: :depends r-data.table: :depends r-dplyr: :depends r-dynamictreecut: :depends r-getopt: :depends r-ggplot2: :depends r-gplots: :depends r-gsubfn: :depends r-seqinr: :depends readline: ``>=6.2`` :depends roary: :depends samtools: :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 smeg and update with:: mamba update smeg To create a new environment, run:: mamba create --name myenvname smeg 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/smeg: (see `smeg/tags`_ for valid values for ````) .. |downloads_smeg| image:: https://img.shields.io/conda/dn/bioconda/smeg.svg?style=flat :target: https://anaconda.org/bioconda/smeg :alt: (downloads) .. |docker_smeg| image:: https://quay.io/repository/biocontainers/smeg/status :target: https://quay.io/repository/biocontainers/smeg .. _`smeg/tags`: https://quay.io/repository/biocontainers/smeg?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/smeg/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/smeg/README.html