:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'expansionhunterdenovo' .. highlight: bash expansionhunterdenovo ===================== .. conda:recipe:: expansionhunterdenovo :replaces_section_title: :noindex: ExpansionHunter Denovo \(EHdn\) is a suite of tools for detecting novel expansions of short tandem repeats \(STRs\). :homepage: https://github.com/Illumina/ExpansionHunterDenovo :license: Apache License 2.0 :recipe: /`expansionhunterdenovo `_/`meta.yaml `_ .. conda:package:: expansionhunterdenovo |downloads_expansionhunterdenovo| |docker_expansionhunterdenovo| :versions: ``0.9.0-7``,  ``0.9.0-6``,  ``0.9.0-5``,  ``0.9.0-4``,  ``0.9.0-3``,  ``0.9.0-2``,  ``0.9.0-1``,  ``0.9.0-0`` :depends backports.lzma: :depends boost-cpp: ``>=1.78.0,<1.78.1.0a0`` :depends bzip2: ``>=1.0.8,<2.0a0`` :depends cmake: :depends htslib: ``>=1.17,<1.20.0a0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends spdlog: ``1.4.2.*`` :depends zlib: :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 expansionhunterdenovo and update with:: mamba update expansionhunterdenovo To create a new environment, run:: mamba create --name myenvname expansionhunterdenovo 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/expansionhunterdenovo: (see `expansionhunterdenovo/tags`_ for valid values for ````) .. |downloads_expansionhunterdenovo| image:: https://img.shields.io/conda/dn/bioconda/expansionhunterdenovo.svg?style=flat :target: https://anaconda.org/bioconda/expansionhunterdenovo :alt: (downloads) .. |docker_expansionhunterdenovo| image:: https://quay.io/repository/biocontainers/expansionhunterdenovo/status :target: https://quay.io/repository/biocontainers/expansionhunterdenovo .. _`expansionhunterdenovo/tags`: https://quay.io/repository/biocontainers/expansionhunterdenovo?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/expansionhunterdenovo/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/expansionhunterdenovo/README.html