recipe sniffles

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore).

Homepage:

https://github.com/fritzsedlazeck/Sniffles

Documentation:

https://github.com/fritzsedlazeck/Sniffles/wiki

License:

MIT / MIT

Recipe:

/sniffles/meta.yaml

Links:

doi: 10.1038/s41587-023-02024-y, doi: 10.1038/s41592-018-0001-7, biotools: sniffles, usegalaxy-eu: sniffles

package sniffles

(downloads) docker_sniffles

versions:
2.5.3-0,  2.5.2-0,  2.4-0,  2.3.3-0,  2.3.2-1,  2.3.2-0,  2.2-0,  2.0.7-0,  2.0.6-0, 

2.5.3-0,  2.5.2-0,  2.4-0,  2.3.3-0,  2.3.2-1,  2.3.2-0,  2.2-0,  2.0.7-0,  2.0.6-0,  2.0.5-0,  2.0.4-0,  2.0.3-0,  2.0.2-0,  1.0.12-1,  1.0.12-0,  1.0.11-1,  1.0.11-0,  1.0.10-0,  1.0.8-0,  1.0.7-1,  1.0.7-0,  1.0.6-0,  1.0.5-0,  1.0.3-0

depends psutil:

>=5.9.4

depends pysam:

>=0.21.0

depends python:

>=3.10

depends python-edlib:

>=1.3.9

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 sniffles

and update with::

   mamba update sniffles

To create a new environment, run:

mamba create --name myenvname sniffles

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/sniffles:<tag>

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

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