:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'tetyper' .. highlight: bash tetyper ======= .. conda:recipe:: tetyper :replaces_section_title: :noindex: Typing of a specific transposable element \(TE\) of interest from paired\-end sequencing data. :homepage: https://github.com/aesheppard/TETyper :license: GPL-3.0 :recipe: /`tetyper `_/`meta.yaml `_ :links: doi: :doi:`10.1099/mgen.0.000232` .. conda:package:: tetyper |downloads_tetyper| |docker_tetyper| :versions: ``1.1-1``,  ``1.1-0`` :depends bcftools: :depends biopython: :depends blast: :depends bwa: :depends pysam: :depends python: :depends pyvcf: :depends samtools: :depends spades: :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 tetyper and update with:: mamba update tetyper To create a new environment, run:: mamba create --name myenvname tetyper 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/tetyper: (see `tetyper/tags`_ for valid values for ````) .. |downloads_tetyper| image:: https://img.shields.io/conda/dn/bioconda/tetyper.svg?style=flat :target: https://anaconda.org/bioconda/tetyper :alt: (downloads) .. |docker_tetyper| image:: https://quay.io/repository/biocontainers/tetyper/status :target: https://quay.io/repository/biocontainers/tetyper .. _`tetyper/tags`: https://quay.io/repository/biocontainers/tetyper?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/tetyper/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/tetyper/README.html