recipe mobster

NGS tool for detecting MEI and gene retrotransposition events in WGS and WES data, see Thung et al. Genome Biol. 2014 for more information.

Homepage:

https://github.com/jyhehir/mobster

License:

GPL3

Recipe:

/mobster/meta.yaml

package mobster

(downloads) docker_mobster

versions:

0.2.4.1-1,  0.2.4.1-0,  0.2.3.1-0,  0.2.2-1,  0.2.2-0,  0.2.1-0

depends mosaik:

depends openjdk:

depends python:

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 mobster

and update with::

   mamba update mobster

To create a new environment, run:

mamba create --name myenvname mobster

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/mobster:<tag>

(see `mobster/tags`_ for valid values for ``<tag>``)

Notes

After installation, mobster is available as command `mobster`. Further, you can convert mobster output to vcf with the command `mobster-to-vcf`.

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Link to this page

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