Fix config.json issues

.gitlab-ci.yml

@@ -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

image/Dockerfile

@@ -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