recipe savana

SAVANA: a somatic structural variant caller for long-read data

Homepage:

https://github.com/cortes-ciriano-lab/savana

License:

Apache-2.0

Recipe:

/savana/meta.yaml

package savana

versions:

1.2.5-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.0.5-0,  1.0.4-0, 

1.2.5-0,  1.2.4-0,  1.2.3-0,  1.2.2-0,  1.2.1-0,  1.2.0-1,  1.2.0-0,  1.0.5-0,  1.0.4-0,  1.0.3-0,  1.0.0-0,  0.2.3-0,  0.2.1-0

depends cyvcf2:

>=0.30.16

depends matplotlib-base:

>=3.7.1

depends pandas:

>=2.0.0

depends pybedtools:

>=0.9.0

depends pysam:

>=0.20.0

depends python:

>=3.9

depends scikit-learn:

1.2.2.*

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 savana

and update with::

   mamba update savana

To create a new environment, run:

mamba create --name myenvname savana

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/savana:<tag>

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

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