recipe svim

SVIM is a structural variant caller for long reads.

Homepage:

https://pypi.org/project/svim/

Documentation:

https://github.com/eldariont/svim/wiki

Developer docs:

https://github.com/eldariont/svim

License:

GPL / GPL-3.0

Recipe:

/svim/meta.yaml

Links:

doi: 10.1093/bioinformatics/btz041

package svim

versions:

2.0.0-0,  1.4.2-0,  1.4.1-0,  1.4.0-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.1-0,  1.1.0-0, 

2.0.0-0,  1.4.2-0,  1.4.1-0,  1.4.0-0,  1.3.1-0,  1.3.0-0,  1.2.0-0,  1.1.1-0,  1.1.0-0,  1.0.0-0,  0.5.0-0,  0.4.4-0,  0.4.3-0,  0.4.2-0,  0.4.1-0

depends matplotlib-base:

>=3.3.0

depends minimap2:

depends networkx:

depends ngmlr:

depends numpy:

depends py-cpuinfo:

>=7.0.0

depends pysam:

>=0.15.2

depends pyspoa:

>=0.0.6

depends python:

>=3.8

depends python-edlib:

depends samtools:

depends scipy:

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 svim

and update with::

   mamba update svim

To create a new environment, run:

mamba create --name myenvname svim

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/svim:<tag>

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

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