recipe duet

SNP-Assisted Structural Variant Calling and Phasing Using Oxford Nanopore Sequencing

Homepage:

https://github.com/yekaizhou/duet

License:

BSD / BSD-3-Clause

Recipe:

/duet/meta.yaml

package duet

versions:

1.0-0,  0.6-0,  0.5-0,  0.4-0,  0.3-0,  0.2-0

depends bcftools:

1.8.*

depends clair3:

1.0.3.*

depends cutesv:

2.0.2.*

depends python:

3.9.0.*

depends sniffles:

2.0.7.*

depends svim:

1.4.2.*

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 duet

and update with::

   mamba update duet

To create a new environment, run:

mamba create --name myenvname duet

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/duet:<tag>

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

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