recipe mageck-vispr

MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens based on MAGeCK, VISPR, Snakemake, FastQC and cutadapt.

Homepage:

https://bitbucket.org/liulab/mageck-vispr

License:

MIT License

Recipe:

/mageck-vispr/meta.yaml

package mageck-vispr

versions:

0.5.6-0,  0.5.5-0,  0.5.4-3,  0.5.4-2,  0.5.4-1,  0.5.4-0,  0.5.3-0,  0.5.2-0,  0.4.7-0, 

0.5.6-0,  0.5.5-0,  0.5.4-3,  0.5.4-2,  0.5.4-1,  0.5.4-0,  0.5.3-0,  0.5.2-0,  0.4.7-0,  0.4.6-0,  0.4.5-0

depends cutadapt:

depends fastqc:

depends jinja2:

depends mageck:

>=0.5.9

depends python:

>=3

depends snakemake:

depends vispr:

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 mageck-vispr

and update with::

   mamba update mageck-vispr

To create a new environment, run:

mamba create --name myenvname mageck-vispr

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/mageck-vispr:<tag>

(see `mageck-vispr/tags`_ for valid values for ``<tag>``)

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Link to this page

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