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Migrate the data version label into the workflow #261

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Merged
MattWellie merged 2 commits into from
Oct 9, 2025
Merged

Migrate the data version label into the workflow #261

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migrate the data version label into the workflow
MattWellie Sep 8, 2025
a6d2ccc
Merge branch 'main' into migrate_data_version_into_workflow
MattWellie Oct 9, 2025
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11 changes: 1 addition & 10 deletions images/exomiser/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
FROM us.gcr.io/broad-gatk/gatk:4.6.2.0

ARG VERSION=14.1.0
ARG DATA_VERSION=2502
ARG VERSION=13.3.0

ENV EXOMISER_STEM="exomiser-cli-${VERSION}"
ENV EXOMISER_ARCHIVE="${EXOMISER_STEM}-distribution.zip"
Expand Down Expand Up @@ -30,11 +29,3 @@ RUN apt-get update && \
pip3 install PyYAML

COPY config_shuffle.py template.yaml ./

# create the application.properties file, responsive to version ARGs
RUN echo "exomiser.data-directory=/exomiser/${EXOMISER_STEM}/data" > /exomiser/${EXOMISER_STEM}/application.properties && \
echo "exomiser.hg38.data-version=${DATA_VERSION}" >> /exomiser/${EXOMISER_STEM}/application.properties && \
echo "exomiser.phenotype.data-version=${DATA_VERSION}" >> /exomiser/${EXOMISER_STEM}/application.properties && \
echo "exomiser.hg38.clin-var-data-version=${DATA_VERSION}" >> /exomiser/${EXOMISER_STEM}/application.properties && \
echo "exomiser.hg38.use-clinvar-white-list=true" >> /exomiser/${EXOMISER_STEM}/application.properties && \
echo "logging.level.com.zaxxer.hikari=ERROR" >> /exomiser/${EXOMISER_STEM}/application.properties