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
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install spectacle
and update with:
conda update spectacle
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.
A Docker container is available at https://quay.io/repository/biocontainers/spectacle.