# Stage 1: Jbrowse config file generated FROM quay.io/biocontainers/jbrowse2:2.15.3--hbbc3ce4_0 as jbrowse_base WORKDIR /app COPY jbrowse_script_base.sh . RUN ./jbrowse_script_base.sh \ && rm jbrowse_script_base.sh RUN rm -rf annelids/node_modules # Stage 2: Json processing FROM ghcr.io/jqlang/jq:1.7.1 as jbrowse_builder WORKDIR /app/annelids COPY --from=jbrowse_base /app/annelids/ /app/annelids/ COPY default_session.json tracks.json ./ RUN --argfile base default_session.json '.defaultSession = $base' < config.json > config.json # | jq --argfile base tracks.json '. += $base' > config.json \ # && rm default_session.json tracks.json # Stage 3: Load into nginx FROM nginx:alpine WORKDIR /usr/share/nginx/html RUN rm -rf ./* COPY --from=jbrowse_builder /app/annelids/ . ENTRYPOINT ["nginx", "-g", "daemon off;"]