recipe mavis

A Structural Variant Post-Processing Package.

Homepage:

https://github.com/bcgsc/mavis

Documentation:

http://mavis.bcgsc.ca/docs/latest

License:

GPL3 / GPL-3.0-or-later

Recipe:

/mavis/meta.yaml

package mavis

versions:

3.1.2-0,  2.2.6-0

depends biopython:

>=1.70,<1.78

depends braceexpand:

0.1.2

depends colour:

depends distance:

>=0.1.3

depends mavis-config:

>=1.2.2

depends networkx:

>=2.5,<3

depends numpy:

>=1.13.1

depends pandas:

>=1.1,<2

depends pysam:

depends python:

>=3.7

depends shapely:

>=1.6.4.post1

depends shortuuid:

>=0.5.0

depends svgwrite:

depends typing-extensions:

>=4

depends ucsc-blat:

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 mavis

and update with::

   mamba update mavis

To create a new environment, run:

mamba create --name myenvname mavis

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/mavis:<tag>

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

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