- recipe spectacle
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:
- License:
GPL / GPL-3.0
- Recipe:
- package spectacle¶
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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:<tag> (see `spectacle/tags`_ for valid values for ``<tag>``)
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¶
Link to this page¶
Render an 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)