recipe severus

A tool for somatic structural variant calling using long reads

Homepage:

https://github.com/KolmogorovLab/Severus

License:

BSD-3-Clause

Recipe:

/severus/meta.yaml

package severus

versions:

1.0-0,  0.1.2-0,  0.1.1-0

depends biopython:

depends matplotlib-base:

depends networkx:

>=2.6

depends numpy:

depends pip:

depends plotly:

depends pydot:

depends pygraphviz:

depends pysam:

depends python:

>=3.8

depends samtools:

>=1.14

depends setuptools:

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 severus

and update with::

   mamba update severus

To create a new environment, run:

mamba create --name myenvname severus

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/severus:<tag>

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

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