recipe cistrome-ceas

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

package cistrome-ceas

(downloads) 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:

additional platforms:

Installation

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 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:<tag>

(see `cistrome-ceas/tags`_ for valid values for ``<tag>``)

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

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