recipe duphold

SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls.

Homepage:

https://github.com/brentp/duphold

License:

MIT

Recipe:

/duphold/meta.yaml

package duphold

(downloads) docker_duphold

versions:
0.2.1-4,  0.2.1-3,  0.2.1-2,  0.2.1-1,  0.2.1-0,  0.2.0-0,  0.1.4-0,  0.1.3-0,  0.1.2-0, 

0.2.1-4,  0.2.1-3,  0.2.1-2,  0.2.1-1,  0.2.1-0,  0.2.0-0,  0.1.4-0,  0.1.3-0,  0.1.2-0,  0.1.1-0,  0.1.0-0,  0.0.9-0,  0.0.6-0,  0.0.3-0,  0.0.2-0

depends htslib:

>=1.9,<1.10.0a0

depends libgcc-ng:

>=12

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 duphold

and update with::

   mamba update duphold

To create a new environment, run:

mamba create --name myenvname duphold

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/duphold:<tag>

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

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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