recipe cellxgene

Web application for exploration of large scale scRNA-seq datasets

Homepage:

https://chanzuckerberg.github.io/cellxgene/

Documentation:

https://github.com/chanzuckerberg/cellxgene

License:

MIT / MIT

Recipe:

/cellxgene/meta.yaml

Links:

usegalaxy-eu: interactive_tool_cellxgene

package cellxgene

versions:

1.3.0-0,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.1-0,  1.0.0-0,  0.16.7-0,  0.16.6-0, 

1.3.0-0,  1.2.0-0,  1.1.2-0,  1.1.1-0,  1.1.0-0,  1.0.1-0,  1.0.0-0,  0.16.7-0,  0.16.6-0,  0.16.5-0,  0.16.4-0,  0.16.2-0,  0.16.0-0

depends anndata:

>=0.7.6

depends boto3:

>=1.12.18

depends click:

>=7.1.2

depends fastobo:

>=0.6.1

depends flask:

>=1.0.2

depends flask-compress:

>=1.4.0

depends flask-cors:

>=3.0.9

depends flask-restful:

>=0.3.6

depends flask-server-timing:

>=0.1.2

depends flask-talisman:

>=0.7.0

depends flatten-dict:

>=0.2.0

depends fsspec:

>=0.4.4,<0.8.0

depends gunicorn:

>=20.0.4

depends h5py:

>=3.0.0

depends numba:

>=0.51.2

depends numpy:

>=1.17.5

depends packaging:

>=20.0

depends pandas:

>=1.0,!=1.1

depends python:

>=3.6,<3.12

depends python-flatbuffers:

>=1.11.0,<2.0.0

depends pyyaml:

>=5.4

depends requests:

>=2.22.0

depends s3fs:

0.4.2

depends scipy:

>=1.4.0

depends sqlalchemy:

depends tiledb-py:

>=0.6.2

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 cellxgene

and update with::

   mamba update cellxgene

To create a new environment, run:

mamba create --name myenvname cellxgene

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/cellxgene:<tag>

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

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Link to this page

Render an 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/cellxgene/README.html)