:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'a5-miseq' .. highlight: bash a5-miseq ======== .. conda:recipe:: a5-miseq :replaces_section_title: :noindex: A5\-miseq is a pipeline for assembling DNA sequence data generated on the Illumina sequencing platform. This README will take you through the steps necessary for running \_A5\-miseq\_ :homepage: https://sourceforge.net/projects/ngop :license: GPLv3 :recipe: /`a5-miseq `_/`meta.yaml `_ .. conda:package:: a5-miseq |downloads_a5-miseq| |docker_a5-miseq| :versions: ``20160825-2``,  ``20160825-1``,  ``20160825-0`` :depends openjdk: ``>=8.0`` :depends perl: :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 a5-miseq and update with:: mamba update a5-miseq To create a new environment, run:: mamba create --name myenvname a5-miseq 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/a5-miseq: (see `a5-miseq/tags`_ for valid values for ````) .. |downloads_a5-miseq| image:: https://img.shields.io/conda/dn/bioconda/a5-miseq.svg?style=flat :target: https://anaconda.org/bioconda/a5-miseq :alt: (downloads) .. |docker_a5-miseq| image:: https://quay.io/repository/biocontainers/a5-miseq/status :target: https://quay.io/repository/biocontainers/a5-miseq .. _`a5-miseq/tags`: https://quay.io/repository/biocontainers/a5-miseq?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/a5-miseq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/a5-miseq/README.html