recipe snapatac2

Python/Rust package for single-cell epigenomics analysis

Homepage:

https://github.com/kaizhang/SnapATAC2

Documentation:

https://kzhang.org/SnapATAC2/

License:

MIT / MIT

Recipe:

/snapatac2/meta.yaml

Links:

biotools: snapatac, doi: 10.1101/2023.09.11.557221

package snapatac2

versions:

2.5.3-0,  2.5.2-0,  2.5.1-0

depends anndata:

depends h5py:

depends libgcc-ng:

>=12

depends matplotlib-base:

depends numba:

depends numpy:

depends packaging:

depends pandas:

depends pooch:

depends python:

>=3.10,<3.11.0a0

depends python_abi:

3.10.* *_cp310

depends rustworkx:

depends scanpy:

depends scikit-learn:

depends scipy:

depends seaborn:

depends typing_extensions:

depends umap-learn:

requirements:

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 snapatac2

and update with::

   mamba update snapatac2

To create a new environment, run:

mamba create --name myenvname snapatac2

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/snapatac2:<tag>

(see `snapatac2/tags`_ for valid values for ``<tag>``)

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