recipe bioconductor-basilisk

Freezing Python Dependencies Inside Bioconductor Packages






Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.

package bioconductor-basilisk

(downloads) docker_bioconductor-basilisk



depends bioconductor-basilisk.utils:


depends bioconductor-dir.expiry:


depends r-base:


depends r-reticulate:



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 bioconductor-basilisk

and update with::

   mamba update bioconductor-basilisk

To create a new environment, run:

mamba create --name myenvname bioconductor-basilisk

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 `bioconductor-basilisk/tags`_ for valid values for ``<tag>``)

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