recipe wg-blimp

wg-blimp (Whole Genome BisuLfIte sequencing Methylation analysis Pipeline)

Homepage:

https://github.com/MarWoes/wg-blimp

License:

GPL / AGPL-3.0

Recipe:

/wg-blimp/meta.yaml

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 click:

depends h5py:

depends pysam:

depends python:

depends r-base:

depends r-data.table:

depends r-dt:

depends r-ggplot2:

depends r-htmlwidgets:

depends r-httpuv:

depends r-shiny:

depends r-shinydashboard:

depends ruamel.yaml:

depends snakemake-minimal:

>=5.8

requirements:

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 wg-blimp

and update with::

   mamba update wg-blimp

To create a new environment, run:

mamba create --name myenvname wg-blimp

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/wg-blimp:<tag>

(see `wg-blimp/tags`_ for valid values for ``<tag>``)

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