:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'artic' .. highlight: bash artic ===== .. conda:recipe:: artic :replaces_section_title: :noindex: ARTIC pipeline \- a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore :homepage: https://github.com/artic-network/fieldbioinformatics :license: MIT :recipe: /`artic `_/`meta.yaml `_ .. conda:package:: artic |downloads_artic| |docker_artic| :versions: .. raw:: html
1.2.4-11.2.4-01.2.3-01.2.2-01.2.1-01.2.0-01.1.3-11.1.3-01.1.2-0 ``1.2.4-1``,  ``1.2.4-0``,  ``1.2.3-0``,  ``1.2.2-0``,  ``1.2.1-0``,  ``1.2.0-0``,  ``1.1.3-1``,  ``1.1.3-0``,  ``1.1.2-0``,  ``1.1.1-1``,  ``1.1.1-0``,  ``1.1.0_rc2-0`` .. raw:: html
:depends artic-porechop: ``>=0.3.2pre`` :depends artic-tools: :depends bcftools: :depends biopython: :depends bwa: :depends clint: :depends htslib: :depends keras-preprocessing: ``>=1.1.2`` :depends longshot: :depends medaka: ``>=1.10.0`` :depends minimap2: ``>=2.26`` :depends multiqc: :depends muscle: ``3.8.*`` :depends nanopolish: ``>=0.14.0`` :depends pandas: :depends pip: :depends pyfaidx: ``0.6.0.*`` :depends pysam: :depends pytest: :depends python: :depends pyvcf: :depends requests: :depends samtools: :depends tqdm: :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 artic and update with:: mamba update artic To create a new environment, run:: mamba create --name myenvname artic 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/artic: (see `artic/tags`_ for valid values for ````) .. |downloads_artic| image:: https://img.shields.io/conda/dn/bioconda/artic.svg?style=flat :target: https://anaconda.org/bioconda/artic :alt: (downloads) .. |docker_artic| image:: https://quay.io/repository/biocontainers/artic/status :target: https://quay.io/repository/biocontainers/artic .. _`artic/tags`: https://quay.io/repository/biocontainers/artic?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/artic/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/artic/README.html