recipe sistem

A tool for simulating tumor growth, metastasis, and DNA-seq data.

Homepage:

https://github.com/samsonweiner/sistem

Documentation:

https://sistem.readthedocs.io/en/latest

License:

GPL3 / GPL-3.0-only

Recipe:

/sistem/meta.yaml

SISTEM (SImulation of Single-cell Tumor Evolution and Metastasis) is a software package and mathematical model for simulating tumor evolution, cell migrations, and DNA-seq data at single-cell resolution.

package sistem

(downloads) docker_sistem

versions:

1.0.3-0

depends biopython:

>=1.8.1

depends dwgsim:

depends numpy:

>=1.24.3

depends pyfaidx:

>=0.7.2.1

depends python:

>=3.9

depends samtools:

depends scikit-learn:

>=1.6.1

depends scipy:

>=1.10.1

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 sistem

and update with::

   mamba update sistem

To create a new environment, run:

mamba create --name myenvname sistem

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/sistem:<tag>

(see `sistem/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/sistem/README.html)