- recipe cistrome-ceas
Cistrome-CEAS -- Cis-regulatory Element Annotation System
- Homepage:
https://bitbucket.org/cistrome/cistrome-applications-harvard/overview
- Documentation:
- Developer docs:
https://bitbucket.org/cistrome/cistrome-applications-harvard
- License:
Artistic Licence
- Recipe:
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¶
- Versions:
1.0.2b1-2,1.0.2b1-1,1.0.2b1-0- Depends:
on bx-python
on python
<3on r-base
- 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 cistrome-ceas
to add into an existing workspace instead, run:
pixi add cistrome-ceas
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 cistrome-ceas
Alternatively, to install into a new environment, run:
conda create -n envname cistrome-ceas
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/cistrome-ceas:<tag>
(see cistrome-ceas/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¶
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¶
Link to this page¶
Render an 
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