:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'savage' .. highlight: bash savage ====== .. conda:recipe:: savage :replaces_section_title: :noindex: SAVAGE \(Strain Aware VirAl GEnome assembly\) reconstructs individual \(viral\) haplotypes from a mixed sample. :homepage: https://github.com/HaploConduct/HaploConduct/tree/master/savage :license: GPL v3 :recipe: /`savage `_/`meta.yaml `_ .. conda:package:: savage |downloads_savage| |docker_savage| :versions: .. raw:: html
0.4.2-20.4.2-10.4.2-00.4.1-00.4.0-20.4.0-10.4.0-00.3.0-00.2.1-1 ``0.4.2-2``,  ``0.4.2-1``,  ``0.4.2-0``,  ``0.4.1-0``,  ``0.4.0-2``,  ``0.4.0-1``,  ``0.4.0-0``,  ``0.3.0-0``,  ``0.2.1-1``,  ``0.2.1-0`` .. raw:: html
:depends _openmp_mutex: ``>=4.5`` :depends boost-cpp: ``>=1.74.0,<1.74.1.0a0`` :depends bwa: :depends kallisto: ``>=0.43.0`` :depends libgcc-ng: ``>=12`` :depends libstdcxx-ng: ``>=12`` :depends python: ``>=2.7,<2.8.0a0`` :depends python_abi: ``2.7.* *_cp27mu`` :depends rust-overlaps: :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 savage and update with:: mamba update savage To create a new environment, run:: mamba create --name myenvname savage 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/savage: (see `savage/tags`_ for valid values for ````) .. |downloads_savage| image:: https://img.shields.io/conda/dn/bioconda/savage.svg?style=flat :target: https://anaconda.org/bioconda/savage :alt: (downloads) .. |docker_savage| image:: https://quay.io/repository/biocontainers/savage/status :target: https://quay.io/repository/biocontainers/savage .. _`savage/tags`: https://quay.io/repository/biocontainers/savage?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/savage/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/savage/README.html