:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'chromhmm' .. highlight: bash chromhmm ======== .. conda:recipe:: chromhmm :replaces_section_title: :noindex: 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: https://github.com/jernst98/ChromHMM :license: GPLv3 :recipe: /`chromhmm `_/`meta.yaml `_ :links: biotools: :biotools:`chromhmm` .. conda:package:: chromhmm |downloads_chromhmm| |docker_chromhmm| :versions: .. raw:: html
1.25-01.24-01.23-01.21-11.21-01.20-11.20-01.19-01.15-0 ``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`` .. raw:: html
:depends fonts-conda-ecosystem: :depends openjdk: :depends unzip: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/chromhmm: (see `chromhmm/tags`_ for valid values for ````) .. |downloads_chromhmm| image:: https://img.shields.io/conda/dn/bioconda/chromhmm.svg?style=flat :target: https://anaconda.org/bioconda/chromhmm :alt: (downloads) .. |docker_chromhmm| image:: https://quay.io/repository/biocontainers/chromhmm/status :target: https://quay.io/repository/biocontainers/chromhmm .. _`chromhmm/tags`: https://quay.io/repository/biocontainers/chromhmm?tab=tags .. raw:: html 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 ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/chromhmm/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/chromhmm/README.html