- recipe chromhmm
ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks.
- Homepage:
- License:
GPLv3
- Recipe:
- Links:
biotools: chromhmm
- package chromhmm¶
- Versions:
1.27-0,1.26-0,1.25-0,1.24-0,1.23-0,1.21-1,1.21-0,1.20-1,1.20-0,1.27-0,1.26-0,1.25-0,1.24-0,1.23-0,1.21-1,1.21-0,1.20-1,1.20-0,1.19-0,1.15-0,1.14-0,1.12-0,1.11-0- Depends:
on fonts-conda-ecosystem
on openjdk
on unzip
- 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 chromhmm
to add into an existing workspace instead, run:
pixi add chromhmm
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 chromhmm
Alternatively, to install into a new environment, run:
conda create -n envname chromhmm
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/chromhmm:<tag>
(see chromhmm/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¶
ChromHMM comes with about 36MB of example data which is not included in the recipe. This recipe installs a script, "download_chromhmm_data.sh", which downloads the data in the proper location, and which can be run after ChromHMM has been installed.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/chromhmm/README.html)
