:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'phyloflash' .. highlight: bash phyloflash ========== .. conda:recipe:: phyloflash :replaces_section_title: :noindex: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina \(meta\)genomic dataset. :homepage: https://github.com/HRGV/phyloFlash :license: GPL / GPLv3 :recipe: /`phyloflash `_/`meta.yaml `_ .. conda:package:: phyloflash |downloads_phyloflash| |docker_phyloflash| :versions: .. raw:: html
3.4.2-13.4.2-03.4.1-03.4-13.4-03.3b4-03.3b3-03.3b2-03.3b1-1 ``3.4.2-1``,  ``3.4.2-0``,  ``3.4.1-0``,  ``3.4-1``,  ``3.4-0``,  ``3.3b4-0``,  ``3.3b3-0``,  ``3.3b2-0``,  ``3.3b1-1``,  ``3.3b1-0``,  ``3.0b1-1``,  ``3.0b1-0``,  ``2.0beta6-0`` .. raw:: html
:depends bbmap: :depends bedtools: :depends emirge: :depends mafft: :depends perl: ``>=5.13.2`` :depends pigz: :depends r-base: ``>=4.0.0`` :depends r-ggdendro: :depends r-ggplot2: ``>=3.3.0`` :depends r-gtable: :depends r-optparse: :depends r-reshape2: :depends samtools: ``>=1.12`` :depends spades: :depends vsearch: ``>=2.5.0`` :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 phyloflash and update with:: mamba update phyloflash To create a new environment, run:: mamba create --name myenvname phyloflash 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/phyloflash: (see `phyloflash/tags`_ for valid values for ````) .. |downloads_phyloflash| image:: https://img.shields.io/conda/dn/bioconda/phyloflash.svg?style=flat :target: https://anaconda.org/bioconda/phyloflash :alt: (downloads) .. |docker_phyloflash| image:: https://quay.io/repository/biocontainers/phyloflash/status :target: https://quay.io/repository/biocontainers/phyloflash .. _`phyloflash/tags`: https://quay.io/repository/biocontainers/phyloflash?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/phyloflash/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/phyloflash/README.html