:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'nanomonsv' .. highlight: bash nanomonsv ========= .. conda:recipe:: nanomonsv :replaces_section_title: :noindex: Python tools for detecting structural variation from nanopore sequence data :homepage: https://github.com/friend1ws/nanomonsv :license: GPL-3.0 :recipe: /`nanomonsv `_/`meta.yaml `_ .. conda:package:: nanomonsv |downloads_nanomonsv| |docker_nanomonsv| :versions: ``0.7.0-0``,  ``0.6.0-0``,  ``0.5.1-0``,  ``0.5.0-0`` :depends bedtools: ``2.30.0.*`` :depends bwa: ``0.7.17.*`` :depends htslib: ``1.15.*`` :depends mafft: ``7.407.*`` :depends minimap2: ``2.24.*`` :depends numpy: ``1.23.0.*`` :depends parasail-python: ``1.2.4.*`` :depends pysam: ``0.19.1.*`` :depends python: ``>=3.6`` :depends racon: ``1.4.3.*`` :depends repeatmasker: ``4.1.1.*`` :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 nanomonsv and update with:: mamba update nanomonsv To create a new environment, run:: mamba create --name myenvname nanomonsv 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/nanomonsv: (see `nanomonsv/tags`_ for valid values for ````) .. |downloads_nanomonsv| image:: https://img.shields.io/conda/dn/bioconda/nanomonsv.svg?style=flat :target: https://anaconda.org/bioconda/nanomonsv :alt: (downloads) .. |docker_nanomonsv| image:: https://quay.io/repository/biocontainers/nanomonsv/status :target: https://quay.io/repository/biocontainers/nanomonsv .. _`nanomonsv/tags`: https://quay.io/repository/biocontainers/nanomonsv?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/nanomonsv/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/nanomonsv/README.html