:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'spectacle' .. highlight: bash spectacle ========= .. conda:recipe:: spectacle :replaces_section_title: :noindex: This software implements a spectral learning algorithm for hidden Markov models for epigenomic data. Please see our paper for further details\: Song\, J and Chen\, K. C. Spectacle\: fast chromatin state annotation using spectral learning. Genome Biology\, 16\:33\, 2015. http\:\/\/genomebiology.com\/2015\/16\/1\/33 :homepage: https://github.com/jiminsong/Spectacle :license: GPL / GPL-3.0 :recipe: /`spectacle `_/`meta.yaml `_ .. conda:package:: spectacle |downloads_spectacle| |docker_spectacle| :versions: ``1.4-3``,  ``1.4-2``,  ``1.4-1``,  ``1.4-0`` :depends numpy: :depends openjdk: :depends python: :depends scipy: :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 spectacle and update with:: mamba update spectacle To create a new environment, run:: mamba create --name myenvname spectacle 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/spectacle: (see `spectacle/tags`_ for valid values for ````) .. |downloads_spectacle| image:: https://img.shields.io/conda/dn/bioconda/spectacle.svg?style=flat :target: https://anaconda.org/bioconda/spectacle :alt: (downloads) .. |docker_spectacle| image:: https://quay.io/repository/biocontainers/spectacle/status :target: https://quay.io/repository/biocontainers/spectacle .. _`spectacle/tags`: https://quay.io/repository/biocontainers/spectacle?tab=tags .. raw:: html Notes ----- The Spectacle github repo weighs in at around 500MB\, a large portion of which is data files. These have been removed from the conda recipe\, but a script \(download\_spectacle\_data.sh\) has been included here which will download those files from github. In addition\, a wrapper script \`Spectacle.sh\` has been included in this recipe and should be used when calling the program. 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/spectacle/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/spectacle/README.html