recipe smoove

structural variant calling and genotyping with existing tools, but, smoothly

Homepage:

https://github.com/brentp/smoove

License:

Apache / Apache-2.0

Recipe:

/smoove/meta.yaml

package smoove

versions:

0.2.8-1,  0.2.8-0,  0.2.7-0,  0.2.6-1,  0.2.6-0,  0.2.5-0,  0.2.4-0,  0.2.3-1,  0.2.3-0, 

0.2.8-1,  0.2.8-0,  0.2.7-0,  0.2.6-1,  0.2.6-0,  0.2.5-0,  0.2.4-0,  0.2.3-1,  0.2.3-0,  0.1.9-0,  0.1.6-0,  0.1.5-0,  0.1.4-0,  0.1.3-0,  0.1.1-0

depends bcftools:

depends duphold:

depends gsort:

depends htslib:

depends lumpy-sv:

>=0.3

depends mosdepth:

depends samtools:

depends svtools:

depends svtyper:

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 smoove

and update with::

   mamba update smoove

To create a new environment, run:

mamba create --name myenvname smoove

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/smoove:<tag>

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

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Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/smoove/README.html)