:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'purge_dups' .. highlight: bash purge_dups ========== .. conda:recipe:: purge_dups :replaces_section_title: :noindex: purge\_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth. :homepage: https://github.com/dfguan/purge_dups :license: MIT / MIT :recipe: /`purge_dups `_/`meta.yaml `_ .. conda:package:: purge_dups |downloads_purge_dups| |docker_purge_dups| :versions: ``1.2.6-1``,  ``1.2.6-0``,  ``1.2.5-2``,  ``1.2.5-1``,  ``1.2.5-0``,  ``1.0.1-0`` :depends augustus: :depends blast: :depends busco: :depends kmc: :depends libgcc-ng: ``>=12`` :depends libzlib: ``>=1.2.13,<1.3.0a0`` :depends matplotlib-base: :depends minimap2: :depends purge-dups-runner: :depends python: ``>=3.9,<3.10.0a0`` :depends python_abi: ``3.9.* *_cp39`` :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 purge_dups and update with:: mamba update purge_dups To create a new environment, run:: mamba create --name myenvname purge_dups 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/purge_dups: (see `purge_dups/tags`_ for valid values for ````) .. |downloads_purge_dups| image:: https://img.shields.io/conda/dn/bioconda/purge_dups.svg?style=flat :target: https://anaconda.org/bioconda/purge_dups :alt: (downloads) .. |docker_purge_dups| image:: https://quay.io/repository/biocontainers/purge_dups/status :target: https://quay.io/repository/biocontainers/purge_dups .. _`purge_dups/tags`: https://quay.io/repository/biocontainers/purge_dups?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/purge_dups/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/purge_dups/README.html