- recipe wg-blimp
wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline)
- Homepage:
- License:
GPL / AGPL-3.0
- Recipe:
wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline) can be utilised to analyse WGBS data. It performs alignment, qc, methylation calling, DMR calling, segmentation and annotation using a multitude of tools.
- package wg-blimp¶
- Versions:
0.10.0-0,0.9.10-0,0.9.9-0,0.9.8-1,0.9.8-0,0.9.7-0,0.9.6-1,0.9.6-0,0.9.5-1,0.10.0-0,0.9.10-0,0.9.9-0,0.9.8-1,0.9.8-0,0.9.7-0,0.9.6-1,0.9.6-0,0.9.5-1,0.9.5-0,0.9.4-0,0.9.3-0,0.9.2-0,0.9.1-1,0.9.1-0,0.9.0-0- Depends:
on click
on h5py
on pysam
on python
on r-base
on r-data.table
on r-dt
on r-ggplot2
on r-htmlwidgets
on r-httpuv
on r-shiny
on r-shinydashboard
on ruamel.yaml
on snakemake-minimal
>=5.8
- 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 wg-blimp
to add into an existing workspace instead, run:
pixi add wg-blimp
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 wg-blimp
Alternatively, to install into a new environment, run:
conda create -n envname wg-blimp
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/wg-blimp:<tag>
(see wg-blimp/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/wg-blimp/README.html)
