:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'metasv' .. highlight: bash metasv ====== .. conda:recipe:: metasv :replaces_section_title: :noindex: An accurate and integrative structural\-variant caller for next generation sequencing :homepage: https://github.com/bioinform/metasv :license: MIT :recipe: /`metasv `_/`meta.yaml `_ .. conda:package:: metasv |downloads_metasv| |docker_metasv| :versions: ``0.5.4-4``,  ``0.5.4-3``,  ``0.5.4-2``,  ``0.5.4-1``,  ``0.5.4-0``,  ``0.4.0-4``,  ``0.4.0-3`` :depends age-metasv: :depends libgcc-ng: ``>=10.3.0`` :depends pybedtools: ``0.6.9`` :depends pysam: ``0.7.7`` :depends python: ``>=2.7,<2.8.0a0`` :depends python_abi: ``2.7.* *_cp27mu`` :depends pyvcf: ``0.6.7`` :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 metasv and update with:: mamba update metasv To create a new environment, run:: mamba create --name myenvname metasv 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/metasv: (see `metasv/tags`_ for valid values for ````) .. |downloads_metasv| image:: https://img.shields.io/conda/dn/bioconda/metasv.svg?style=flat :target: https://anaconda.org/bioconda/metasv :alt: (downloads) .. |docker_metasv| image:: https://quay.io/repository/biocontainers/metasv/status :target: https://quay.io/repository/biocontainers/metasv .. _`metasv/tags`: https://quay.io/repository/biocontainers/metasv?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/metasv/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/metasv/README.html