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:

https://github.com/jiminsong/Spectacle

License:

GPL / GPL-3.0

Recipe:

/spectacle/meta.yaml

package spectacle

(downloads) docker_spectacle

versions:

1.4-3,  1.4-2,  1.4-1,  1.4-0

depends numpy:

depends openjdk:

depends python:

depends scipy:

requirements:

additional platforms:

Installation

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.

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