:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'daisysuite' .. highlight: bash daisysuite ========== .. conda:recipe:: daisysuite :replaces_section_title: :noindex: DaisySuite \- mapping\-based pipeline for horizontal gene transfer \(HGT\) detection using sequencing data :homepage: https://gitlab.com/eseiler/DaisySuite :license: GNU GPLv3 :recipe: /`daisysuite `_/`meta.yaml `_ .. conda:package:: daisysuite |downloads_daisysuite| |docker_daisysuite| :versions: ``1.3.0-2``,  ``1.3.0-1``,  ``1.3.0-0``,  ``1.2.1-1``,  ``1.2.1-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.1.0-0``,  ``1.0.0-0`` :depends bedtools: ``2.22`` :depends biopython: ``1.72`` :depends bwa: ``0.7.12`` :depends clever-toolkit: ``2.0rc3`` :depends gustaf: ``1.0.8`` :depends mason: ``2.0.7`` :depends pandas: ``0.18.1`` :depends pysam: ``0.9.1.4`` :depends sak: ``0.4.6`` :depends samtools: ``1.9`` :depends scipy: ``1.1.0`` :depends snakemake: ``3.9.0`` :depends stellar: ``1.4.9`` :depends yara: ``0.9.6`` :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 daisysuite and update with:: mamba update daisysuite To create a new environment, run:: mamba create --name myenvname daisysuite 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/daisysuite: (see `daisysuite/tags`_ for valid values for ````) .. |downloads_daisysuite| image:: https://img.shields.io/conda/dn/bioconda/daisysuite.svg?style=flat :target: https://anaconda.org/bioconda/daisysuite :alt: (downloads) .. |docker_daisysuite| image:: https://quay.io/repository/biocontainers/daisysuite/status :target: https://quay.io/repository/biocontainers/daisysuite .. _`daisysuite/tags`: https://quay.io/repository/biocontainers/daisysuite?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/daisysuite/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/daisysuite/README.html