recipe scrubby

Read depletion/extraction and database cleaning using k-mer and alignment methods

Homepage:

https://github.com/esteinig/scrubby

License:

MIT / MIT

Recipe:

/scrubby/meta.yaml

package scrubby

versions:

0.2.1-0

depends kraken2:

2.1.2.*

depends libgcc-ng:

>=12

depends minimap2:

2.24.*

depends strobealign:

0.8.0.*

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 scrubby

and update with::

   mamba update scrubby

To create a new environment, run:

mamba create --name myenvname scrubby

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/scrubby:<tag>

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

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