:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'pavfinder' .. highlight: bash pavfinder ========= .. conda:recipe:: pavfinder :replaces_section_title: :noindex: PAVFinder is a Python package that detects structural variants from de novo assemblies. :homepage: https://github.com/bcgsc/pavfinder :license: GPL-3.0 :recipe: /`pavfinder `_/`meta.yaml `_ :links: doi: :doi:`10.1186/s12920-018-0402-6`, doi: :doi:`10.1093/bioinformatics/btz902` .. conda:package:: pavfinder |downloads_pavfinder| |docker_pavfinder| :versions: ``1.8.5-0`` :depends bash: :depends biobloomtools: :depends biopython: :depends blast: :depends bwa: :depends gmap: :depends intspan: ``>=0.701`` :depends make: :depends pybedtools: ``>=0.6.9`` :depends pysam: ``>=0.8.1`` :depends python: ``>=3`` :depends rnabloom: :depends ruffus: :depends samtools: :depends transabyss: :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 pavfinder and update with:: mamba update pavfinder To create a new environment, run:: mamba create --name myenvname pavfinder 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/pavfinder: (see `pavfinder/tags`_ for valid values for ````) .. |downloads_pavfinder| image:: https://img.shields.io/conda/dn/bioconda/pavfinder.svg?style=flat :target: https://anaconda.org/bioconda/pavfinder :alt: (downloads) .. |docker_pavfinder| image:: https://quay.io/repository/biocontainers/pavfinder/status :target: https://quay.io/repository/biocontainers/pavfinder .. _`pavfinder/tags`: https://quay.io/repository/biocontainers/pavfinder?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/pavfinder/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/pavfinder/README.html