jdelafon/gemini repository overview

Image for Gemini, the variants analysis tool from https://github.com/arq5x/gemini⁠. The tag represents the version of Gemini.

Based on Python 2.7. All it does is download the automatic installation script and run it. Source: https://gitlab.com/jdelafon/gemini⁠

!! The annotation functionality is broken in the "0.30.2" image !! (in Gemini itself, because of the version of Pysam pulled by Conda in the automatic installation process), see https://github.com/arq5x/gemini/issues/951⁠. This is why there is a "-patched" image that contains a dirty fix to still be able to use it.

Basic usage:

docker run jdelafon/gemini -v

Annotation databases are not included, but expected to be mounted to /usr/local/share/gemini/gemini_data, for instance:

docker run \
-v $(pwd)/gemini_data:/usr/local/share/gemini/gemini_data \
jdelafon/gemini

This is necessary to overcome the 5GB limit in Docker containers, and also because you probably want to persist this data (in this example, it is present/gets downloaded to $(pwd)/gemini_data on the host).

Similarly, with a volume mounted, you can install additional annotation dbs with for example

docker run \
-v $(pwd)/gemini_data:/usr/local/share/gemini/gemini_data \
jdelafon/gemini update --dataonly --extra cadd_score

Annotation example, assuming your annotation files are in a host directory ./gemini_data and your VFC source files (.vcf, .ped) are in ./datasets:

docker run -it --rm --name gemini \
-v $(pwd)/gemini_data:/usr/local/share/gemini/gemini_data \
-v $(pwd)/datasets:/datasets \
gemini load -t VEP -v /datasets/test.vep.vcf.gz -p /datasets/test.ped /datasets/test.db