- recipe cassiopeia
An end-to-end pipeline for single-cell lineage tracing experiments.
- Homepage:
- License:
MIT / MIT
- Recipe:
- package cassiopeia¶
- versions:
2.0.0-2,2.0.0-1,2.0.0-0- depends biopython:
>=1.71- depends bokeh:
>=0.12.15- depends ccphylo:
- depends ete3:
>=3.1.1- depends hits:
- depends itolapi:
- depends libgcc:
>=13- depends matplotlib-base:
>=2.2.2- depends nbconvert:
>=5.4.0- depends nbformat:
>=4.4.0- depends networkx:
>=2.5- depends ngs-tools:
>=1.5.3- depends numba:
>=0.51.0- depends numpy:
>=1.22.4,<2.0a0- depends pandas:
>=1.1.4- depends pysam:
>=0.14.1- depends python:
>=3.10,<3.11.0a0- depends python-levenshtein:
- depends python_abi:
3.10.* *_cp310- depends pyyaml:
>=3.12- depends scipy:
>=1.2.0- depends tqdm:
>=4- depends typing-extensions:
>=3.7.4- requirements:
- additional platforms:
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 cassiopeia and update with:: mamba update cassiopeia
To create a new environment, run:
mamba create --name myenvname cassiopeia
with
myenvnamebeing 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/cassiopeia:<tag> (see `cassiopeia/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/cassiopeia/README.html)
