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VEP Docker: include GeneSplicer binary #1599

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nuno-agostinho
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@nuno-agostinho nuno-agostinho commented Feb 2, 2024

Fixes #1590: compile genesplicer command for use in VEP Docker/Singularity

This only includes the compiled binary and not the associated training data (because of its size). The data still needs to be mounted by the user as usual for a Docker container.

Usage example

Build the Docker image from this modified Dockerfile and run this command inside Docker:

vep --id rs1348242192 --database --force \
    --plugin GeneSplicer,/plugins/GeneSplicer/genesplicer,${human_data}

Ensembl/VEP_plugins#689: Future improvements to GeneSplicer.pm could make this command easier to use.

@nuno-agostinho nuno-agostinho changed the title VEP Docker: Install GeneSplicer binary VEP Docker: include GeneSplicer binary Feb 2, 2024
@nuno-agostinho nuno-agostinho marked this pull request as ready for review February 2, 2024 16:34
@olaaustine
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Hi @nuno-agostinho,
Thank you very much for this change.
This seems fine to me.
Tested on docker using the test example above.
Waiting for the failed tests to pass before merging.
Thank you
Ola.

@olaaustine olaaustine merged commit ab77fad into Ensembl:postreleasefix/112 Feb 19, 2024
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@nuno-agostinho nuno-agostinho deleted the docker/genesplicer branch February 19, 2024 11:16
@olaaustine
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Merged into release/112 and main.

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3 participants