Finish touching up the new Dockerfile with jq

Debug

Try with the right entrypoint

Attempt at fixing

Attempt at fixin #2

Attempt at fixin #3

Attempt at fixin #4

Attempt at fixin #4

Attempt at fixin #5

Attempt at fixin #7

Attempt at fixin #8

.gitlab-ci.yml

@@ -37,7 +37,6 @@ build_nginx_with_jbrowse_config_file:
   stage: build
   image:
     name: gcr.io/kaniko-project/executor:v1.23.2-debug
-    entrypoint: [""]
   before_script:
     # yamllint disable-line rule:line-length
     - echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json

image/Dockerfile

-# 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 0: Get jq
+FROM ghcr.io/jqlang/jq:1.7.1 as jq
 
-# Stage 2: Json processing
-FROM ghcr.io/jqlang/jq:1.7.1 as jbrowse_builder
+# Stage 1: Jbrowse config file generated
+FROM quay.io/biocontainers/jbrowse2:2.15.3--hbbc3ce4_0 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
+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 \
+    && rm -rf node_modules jq jbrowse_script_base.sh default_session.json tracks.json
 
-# Stage 3: Load into nginx
+# Stage 2: Load into nginx
 FROM nginx:alpine
 WORKDIR /usr/share/nginx/html
 RUN rm -rf ./*

image/jbrowse_script_base.sh

 #!/bin/bash -eux
 # Platy only for now
-jbrowse create annelids
-cd annelids
+jbrowse create -f .
 # Assemblies
 jbrowse add-assembly https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz -n "pdumv021" --displayName "Platynereis dumerilii genome v2.1 (pdumv021)" --gziLocation https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz.gzi --faiLocation https://s3.embl.de/annelids/pdumv021/pdumv021.fa.gz.fai -t bgzipFasta
 jbrowse add-assembly https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz -n "pmassv1_masked" --displayName "Platynereis massiliensis genome v1 - masked (pmassv1)" --gziLocation https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.gzi --faiLocation https://s3.embl.de/annelids/pmassv1_masked/pmassv1_masked.fa.gz.fai -t bgzipFasta