recipe cassis

Detection of genomic rearrangement breakpoints






The package Cassis implements methods for precise detection of genomic rearrangement breakpoints, which were described in Lemaitre et al., 2008.

package cassis

(downloads) docker_cassis



depends ghostscript:

depends lastz:

depends perl:

depends r-base:



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 cassis

and update with::

   mamba update cassis

To create a new environment, run:

mamba create --name myenvname cassis

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 `cassis/tags`_ for valid values for ``<tag>``)

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