:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'straglr' .. highlight: bash straglr ======= .. conda:recipe:: straglr :replaces_section_title: :noindex: Short\-tandem repeat genotyping using long reads :homepage: https://github.com/bcgsc/straglr :license: GPL3 / MIT License :recipe: /`straglr `_/`meta.yaml `_ :links: doi: :doi:`10.1186/s13059-021-02447-3` .. conda:package:: straglr |downloads_straglr| |docker_straglr| :versions: ``1.4.1-0``,  ``1.4.0-0``,  ``1.3.0-0``,  ``1.2.0-0``,  ``1.1.1-0`` :depends blast: :depends intspan: ``>=1.5.8`` :depends numpy: ``>=1.14.2`` :depends pathos: ``>=0.2.3`` :depends pybedtools: ``>=0.7.9`` :depends pysam: ``>=0.14.0`` :depends python: :depends scikit-learn: ``>=0.19.0`` :depends scipy: ``>=1.0.1`` :depends trf: :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 straglr and update with:: mamba update straglr To create a new environment, run:: mamba create --name myenvname straglr 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/straglr: (see `straglr/tags`_ for valid values for ````) .. |downloads_straglr| image:: https://img.shields.io/conda/dn/bioconda/straglr.svg?style=flat :target: https://anaconda.org/bioconda/straglr :alt: (downloads) .. |docker_straglr| image:: https://quay.io/repository/biocontainers/straglr/status :target: https://quay.io/repository/biocontainers/straglr .. _`straglr/tags`: https://quay.io/repository/biocontainers/straglr?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/straglr/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/straglr/README.html