:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'cistrome-ceas' .. highlight: bash cistrome-ceas ============= .. conda:recipe:: cistrome-ceas :replaces_section_title: :noindex: Cistrome\-CEAS \-\- Cis\-regulatory Element Annotation System :homepage: https://bitbucket.org/cistrome/cistrome-applications-harvard/overview :documentation: http://liulab.dfci.harvard.edu/CEAS/ :developer docs: https://bitbucket.org/cistrome/cistrome-applications-harvard :license: Artistic Licence :recipe: /`cistrome-ceas `_/`meta.yaml `_ Tool to characterize genome\-wide protein\-DNA interaction patterns from ChIP\-chip and ChIP\-Seq of both sharp and broad binding factors .. conda:package:: cistrome-ceas |downloads_cistrome-ceas| |docker_cistrome-ceas| :versions: ``1.0.2b1-2``,  ``1.0.2b1-1``,  ``1.0.2b1-0`` :depends bx-python: :depends python: ``<3`` :depends r-base: :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 cistrome-ceas and update with:: mamba update cistrome-ceas To create a new environment, run:: mamba create --name myenvname cistrome-ceas 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/cistrome-ceas: (see `cistrome-ceas/tags`_ for valid values for ````) .. |downloads_cistrome-ceas| image:: https://img.shields.io/conda/dn/bioconda/cistrome-ceas.svg?style=flat :target: https://anaconda.org/bioconda/cistrome-ceas :alt: (downloads) .. |docker_cistrome-ceas| image:: https://quay.io/repository/biocontainers/cistrome-ceas/status :target: https://quay.io/repository/biocontainers/cistrome-ceas .. _`cistrome-ceas/tags`: https://quay.io/repository/biocontainers/cistrome-ceas?tab=tags .. raw:: html Notes ----- Installs version 1.0.2 of CEAS from cistrome \(commit id d8c0751\, datestamp 20140929\)\, which includes ceasBW \(a version of ceas which can handle bigWig file input from MACS2\). This version is also patched to suppress warnings about using sqlite3 rather than MySQLdb. The Cistrome code is at https\:\/\/bitbucket.org\/cistrome\/cistrome\-applications\-harvard\/overview The CEAS code is under the published\-packages\/CEAS\/ subdirectory Cistrome data files and documentation can be found at http\:\/\/liulab.dfci.harvard.edu\/CEAS\/index.html 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/cistrome-ceas/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/cistrome-ceas/README.html