:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'purge_haplotigs' .. highlight: bash purge_haplotigs =============== .. conda:recipe:: purge_haplotigs :replaces_section_title: :noindex: Pipeline to help with curating heterozygous diploid genome assemblies. :homepage: https://bitbucket.org/mroachawri/purge_haplotigs/ :license: MIT / MIT :recipe: /`purge_haplotigs `_/`meta.yaml `_ .. conda:package:: purge_haplotigs |downloads_purge_haplotigs| |docker_purge_haplotigs| :versions: ``1.1.3-0``,  ``1.1.2-0``,  ``1.1.1-1``,  ``1.1.1-0``,  ``1.1.0-0``,  ``1.0.4-0``,  ``1.0.3-0``,  ``1.0.1-0`` :depends bedtools: ``>=2.25.0`` :depends make: ``>=4.2.1`` :depends minimap2: ``>=2.12`` :depends perl: ``>=5.22.0`` :depends r-base: ``>=3.4.1`` :depends r-ggplot2: ``>=2.2.1`` :depends samtools: ``>=1.3.1`` :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 purge_haplotigs and update with:: mamba update purge_haplotigs To create a new environment, run:: mamba create --name myenvname purge_haplotigs 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_haplotigs: (see `purge_haplotigs/tags`_ for valid values for ````) .. |downloads_purge_haplotigs| image:: https://img.shields.io/conda/dn/bioconda/purge_haplotigs.svg?style=flat :target: https://anaconda.org/bioconda/purge_haplotigs :alt: (downloads) .. |docker_purge_haplotigs| image:: https://quay.io/repository/biocontainers/purge_haplotigs/status :target: https://quay.io/repository/biocontainers/purge_haplotigs .. _`purge_haplotigs/tags`: https://quay.io/repository/biocontainers/purge_haplotigs?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_haplotigs/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_haplotigs/README.html