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.







biotools: chromhmm

package chromhmm

(downloads) docker_chromhmm



depends fonts-conda-ecosystem:

depends openjdk:

depends unzip:



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 chromhmm

and update with::

   mamba update chromhmm

To create a new environment, run:

mamba create --name myenvname chromhmm

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<tag>

(see `chromhmm/tags`_ for valid values for ``<tag>``)


ChromHMM comes with about 36MB of example data which is not included in the recipe. This recipe installs a script, "", which downloads the data in the proper location, and which can be run after ChromHMM has been installed.

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