recipe ccne

Carbapenemase-encoding gene copy number estimator



GPL / GPL-3.0



package ccne

(downloads) docker_ccne



depends bedtools:


depends blast:


depends bwa:


depends deeptools:


depends htstream:


depends perl:

depends perl-math-cdf:

depends samtools:


depends ucsc-fatotwobit:



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 ccne

and update with::

   mamba update ccne

To create a new environment, run:

mamba create --name myenvname ccne

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<tag>

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

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