recipe snapatac2

SnapATAC2: Single-cell epigenomics analysis pipeline.

Homepage:

https://github.com/kaizhang/SnapATAC2

Documentation:

https://kzhang.org/SnapATAC2

License:

MIT / MIT

Recipe:

/snapatac2/meta.yaml

Links:

biotools: snapatac, doi: 10.1038/s41592-023-02139-9, usegalaxy-eu: snapatac2_preprocessing, usegalaxy-eu: snapatac2_clustering, usegalaxy-eu: snapatac2_peaks_and_motif, usegalaxy-eu: snapatac2_plotting

package snapatac2

(downloads) docker_snapatac2

versions:

2.7.1-0,  2.7.0-0,  2.6.4-0,  2.5.3-0,  2.5.2-0,  2.5.1-0

depends anndata:

depends libgcc:

>=12

depends libzlib:

>=1.2.13,<2.0a0

depends macs3:

depends multiprocess:

depends natsort:

depends numpy:

>=1.16.0

depends pandas:

>=1.0,<2.1.2

depends plotly:

>=5.19.0

depends polars:

>=1.0

depends pooch:

>=1.6.0

depends pyarrow:

depends pyfaidx:

>=0.7.0,<0.8.0

depends python:

>=3.10,<3.11.0a0

depends python-igraph:

>=0.10.3

depends python-kaleido:

depends python_abi:

3.10.* *_cp310

depends rustworkx:

depends scikit-learn:

>=1.0

depends scipy:

>=1.4

depends tqdm:

>=4.62

depends typeguard:

>=4.0

depends typing_extensions:

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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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/snapatac2/README.html)