:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'snvphyl-tools' .. highlight: bash snvphyl-tools ============= .. conda:recipe:: snvphyl-tools :replaces_section_title: :noindex: The SNVPhyl \(Single Nucleotide Variant PHYLogenomics\) pipeline is a pipeline for identifying Single Nucleotide Variants \(SNV\) within a collection of microbial genomes and constructing a phylogenetic tree :homepage: https://github.com/phac-nml/snvphyl-tools :license: apache_2.0 :recipe: /`snvphyl-tools `_/`meta.yaml `_ .. conda:package:: snvphyl-tools |downloads_snvphyl-tools| |docker_snvphyl-tools| :versions: .. raw:: html
1.8.2-81.8.2-71.8.2-61.8.2-51.8.2-41.8.2-31.8.2-21.8.2-11.8.2-0 ``1.8.2-8``,  ``1.8.2-7``,  ``1.8.2-6``,  ``1.8.2-5``,  ``1.8.2-4``,  ``1.8.2-3``,  ``1.8.2-2``,  ``1.8.2-1``,  ``1.8.2-0``,  ``1.8.1-0`` .. raw:: html
:depends bcftools-snvphyl-plugin: ``>=1.9`` :depends grep: :depends libgcc-ng: ``>=12`` :depends mummer: :depends perl: ``>=5.32.1,<5.33.0a0 *_perl5`` :depends perl-bioperl: ``>=1.7.2`` :depends perl-hash-merge: :depends perl-list-moreutils: :depends perl-math-round: :depends perl-parallel-forkmanager: :depends perl-string-util: :depends perl-text-csv: :depends perl-vcftools-vcf: :depends samtools: ``>=1.9`` :depends vcftools: :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 snvphyl-tools and update with:: mamba update snvphyl-tools To create a new environment, run:: mamba create --name myenvname snvphyl-tools 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/snvphyl-tools: (see `snvphyl-tools/tags`_ for valid values for ````) .. |downloads_snvphyl-tools| image:: https://img.shields.io/conda/dn/bioconda/snvphyl-tools.svg?style=flat :target: https://anaconda.org/bioconda/snvphyl-tools :alt: (downloads) .. |docker_snvphyl-tools| image:: https://quay.io/repository/biocontainers/snvphyl-tools/status :target: https://quay.io/repository/biocontainers/snvphyl-tools .. _`snvphyl-tools/tags`: https://quay.io/repository/biocontainers/snvphyl-tools?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/snvphyl-tools/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/snvphyl-tools/README.html