recipe cagecleaner

Genomic redundancy removal tool for cblaster hit sets.

Homepage:

https://github.com/LucoDevro/CAGEcleaner

Documentation:

https://github.com/LucoDevro/CAGEcleaner/wiki

License:

MIT / MIT

Recipe:

/cagecleaner/meta.yaml

Links:

doi: 10.1101/2025.02.19.639057

package cagecleaner

versions:

1.2.2-0,  1.2.1-0,  1.2.0-0

depends biopython:

depends cblaster:

>=1.3.20

depends entrez-direct:

depends ncbi-datasets-cli:

depends pandas:

depends python:

>=3.12

depends scipy:

<=1.14.1

depends skder:

>=1.3.1

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 cagecleaner

and update with::

   mamba update cagecleaner

To create a new environment, run:

mamba create --name myenvname cagecleaner

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/cagecleaner:<tag>

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

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Link to this page

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