:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'biolite' .. highlight: bash biolite ======= .. conda:recipe:: biolite :replaces_section_title: :noindex: A lightweight bioinformatics framework with automated tracking of diagnostics and provenance. :homepage: https://bitbucket.org/caseywdunn/biolite :license: GPLv3 :recipe: /`biolite `_/`meta.yaml `_ .. conda:package:: biolite |downloads_biolite| |docker_biolite| :versions: ``1.2.0-0``,  ``1.1.0-2``,  ``1.1.0-0`` :depends biolite-tools: ``0.4.0`` :depends biopython: ``1.68`` :depends dendropy: ``4.2.0`` :depends docutils: ``0.13.1`` :depends ete3: ``3.0.0b35`` :depends lxml: ``3.7.2`` :depends matplotlib: ``2.0.0`` :depends networkx: ``1.11`` :depends numpy: ``1.11.3`` :depends pandas: ``0.19.2`` :depends python: ``>=2.7,<2.8.0a0`` :depends python-wget: ``3.2`` :depends setuptools: :depends sra-tools: ``2.8.0`` :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 biolite and update with:: mamba update biolite To create a new environment, run:: mamba create --name myenvname biolite 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/biolite: (see `biolite/tags`_ for valid values for ````) .. |downloads_biolite| image:: https://img.shields.io/conda/dn/bioconda/biolite.svg?style=flat :target: https://anaconda.org/bioconda/biolite :alt: (downloads) .. |docker_biolite| image:: https://quay.io/repository/biocontainers/biolite/status :target: https://quay.io/repository/biocontainers/biolite .. _`biolite/tags`: https://quay.io/repository/biocontainers/biolite?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/biolite/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/biolite/README.html