recipe mudskipper

mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.



BSD 3-Clause



package mudskipper

(downloads) docker_mudskipper



depends libgcc-ng:


depends libstdcxx-ng:




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 mudskipper

and update with::

   mamba update mudskipper

To create a new environment, run:

mamba create --name myenvname mudskipper

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

Download stats