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Commit ef09e064 authored by cyril.cros's avatar cyril.cros
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Fix config.json issues

parent 5a73bac5
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......@@ -47,14 +47,6 @@ build_nginx_with_jbrowse_config_file:
- echo "Destination follows"
- echo $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
show_me_my_config:
stage: deploy
image: $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
needs:
- build_nginx_with_jbrowse_config_file
script:
- cat /usr/share/nginx/html/config.json
deploy_to_k8s:
stage: deploy
image: dtzar/helm-kubectl:3.8.2
......
......@@ -4,11 +4,13 @@ FROM ghcr.io/jqlang/jq:1.7.1 as jq
# Stage 1: Jbrowse config file generated
FROM quay.io/biocontainers/jbrowse2:2.15.3--hbbc3ce4_0 as jbrowse_builder
WORKDIR /app/annelids
COPY jbrowse_script_base.sh default_session.json tracks.json ./
COPY --from=jq /jq ./
RUN ./jbrowse_script_base.sh \
&& ./jq --rawfile base default_session.json '.defaultSession = $base' > config.json \
&& ./jq --rawfile base tracks.json '. += $base' > config.json \
COPY jbrowse_script_base.sh ./
RUN ./jbrowse_script_base.sh
COPY tracks.json default_session.json ./
RUN ./jq --rawfile base default_session.json '.defaultSession = $base' config.json > config_tmp.json \
&& ./jq --rawfile base tracks.json '. += $base' config_tmp.json > config_final.json \
&& mv config_final.json config.json \
&& rm -rf node_modules jq jbrowse_script_base.sh default_session.json tracks.json
# Stage 2: Load into nginx
......
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