recipe oncogemini

OncoGEMINI is an adaptation of GEMINI intended for the improved identification of biologically and clincally relevant tumor variants from multi-sample and longitudinal tumor sequencing data






package oncogemini

(downloads) docker_oncogemini



depends cyordereddict:


depends inheritance:


depends numpy:


depends pybedtools:


depends pysam:


depends python:

depends pyyaml:


depends scipy:


depends sqlalchemy:


depends unidecode:


depends vcf2db:

depends vcfanno:



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 oncogemini

and update with::

   mamba update oncogemini

To create a new environment, run:

mamba create --name myenvname oncogemini

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<tag>

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

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