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Last pushed: 2 years ago
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Docker Genevieve - https://github.com/abramconnelly/genevieve
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This is currently a work-in-progress of a Docker image for the Genevieve server. The Docker image has some major functionality missing or broken and should, at this point, be only used for testing and development purposes.

The original Genevieve repository is available at https://github.com/PersonalGenomesOrg/genevieve . The Docker image uses a forked version on my personal GitHub page at https://github.com/abramconnelly/genevieve .

Genevieve

Genevieve is being developed as an open source tool for understanding the
impact of genetic variations. Each variant's interpretation may be edited by
users to form a consensus understanding, generally based upon of existing
literature and other public sources. Genevieve is directly inspired by a
previous open source website used by the
Harvard Personal Genome Project,
GET-Evidence.

Genevieve also enables users to upload genomes and create genome reports that
summarize notable variants within a given genome.

Genevieve's variant database and genome reports are currently limited to
understanding variants listed within
ClinVar.

Launching the Genevieve Docker Image

Currently the best way to launch the Genevieve Docker image is to run it so that output from the various processes get printed to stdout. Initially registration needs a registration link that can be cut-and-pasted into your browser in order to test functionality.

To run:

$ sudo docker run -p 8000:8000 abramconnelly/genevieve:devel

Then point your local web browser to localhost:8000.

$ firefox localhost:80000

From there you can register for an account and watch the output of the running docker container to continue with the validation step of the registration.

Genevieve Web-Interface Usage

The only piece of functionality tested by myself has been the 'import file' functionality. Uploading a valid VCF will eventually result in a CSV report that can be downloaded.

Once registered and logged in, you should be presented with a screen giving you an option to view reports or import a genome. Choosing the import a genome button and uploading a VCF file will ultimately produce a CSV report available through the view reports page.

See the usage instructions for a simple walkthrough of basic usage.

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abramconnelly

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