:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'tirmite' .. highlight: bash tirmite ======= .. conda:recipe:: tirmite :replaces_section_title: :noindex: Map TIR\-pHMM models to genomic sequences for annotation of MITES and complete DNA\-Transposons. :homepage: https://github.com/Adamtaranto/TIRmite :license: MIT / MIT License :recipe: /`tirmite `_/`meta.yaml `_ Build profile Hidden Markov Models for Terminal Inverted repeat families \(TIR\-pHMMs\) and map to genomic sequences for annotation of MITES and complete DNA\-Transposons with variable internal sequence composition. .. conda:package:: tirmite |downloads_tirmite| |docker_tirmite| :versions: ``1.1.4-0``,  ``1.1.3-1``,  ``1.1.3-0``,  ``1.1.1-0``,  ``1.1.0-1``,  ``1.1.0-0`` :depends biopython: ``>=1.70`` :depends pandas: ``>=0.20.3`` :depends pymummer: ``>=0.10.3`` :depends python: ``>=3`` :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 tirmite and update with:: mamba update tirmite To create a new environment, run:: mamba create --name myenvname tirmite 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/tirmite: (see `tirmite/tags`_ for valid values for ````) .. |downloads_tirmite| image:: https://img.shields.io/conda/dn/bioconda/tirmite.svg?style=flat :target: https://anaconda.org/bioconda/tirmite :alt: (downloads) .. |docker_tirmite| image:: https://quay.io/repository/biocontainers/tirmite/status :target: https://quay.io/repository/biocontainers/tirmite .. _`tirmite/tags`: https://quay.io/repository/biocontainers/tirmite?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/tirmite/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/tirmite/README.html