- 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¶
- Versions:
1.4-3,1.4-2,1.4-1,1.4-0- Depends:
on numpy
on openjdk
on python
on scipy
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install spectacle
to add into an existing workspace instead, run:
pixi add spectacle
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install spectacle
Alternatively, to install into a new environment, run:
conda create -n envname spectacle
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/spectacle:<tag>
(see spectacle/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
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:
[](http://bioconda.github.io/recipes/spectacle/README.html)
