:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'gmcloser' .. highlight: bash gmcloser ======== .. conda:recipe:: gmcloser :replaces_section_title: :noindex: GMcloser fills and closes the gaps present in scaffold assemblies\, especially those generated by the de novo assembly of whole genomes with next\-generation sequencing \(NGS\) reads. :homepage: https://sourceforge.net/projects/gmcloser/ :license: GPL / GPL v3 :recipe: /`gmcloser `_/`meta.yaml `_ .. conda:package:: gmcloser |downloads_gmcloser| |docker_gmcloser| :versions: ``1.6.2-1``,  ``1.6.2-0`` :depends blast: :depends bowtie2: :depends mummer: :depends perl: :depends perl-findbin: :depends perl-getopt-long: :depends perl-pod-usage: :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 gmcloser and update with:: mamba update gmcloser To create a new environment, run:: mamba create --name myenvname gmcloser 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/gmcloser: (see `gmcloser/tags`_ for valid values for ````) .. |downloads_gmcloser| image:: https://img.shields.io/conda/dn/bioconda/gmcloser.svg?style=flat :target: https://anaconda.org/bioconda/gmcloser :alt: (downloads) .. |docker_gmcloser| image:: https://quay.io/repository/biocontainers/gmcloser/status :target: https://quay.io/repository/biocontainers/gmcloser .. _`gmcloser/tags`: https://quay.io/repository/biocontainers/gmcloser?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/gmcloser/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/gmcloser/README.html