restructuring to see what happens

image/Dockerfile

@@ -2,16 +2,15 @@
 FROM quay.io/biocontainers/jbrowse2:2.10.2--h5284365_0 as jbrowse_builder
 
 WORKDIR /app
-RUN jbrowse create annelids
-WORKDIR /app/annelids
 COPY jbrowse_script.sh .
 RUN ./jbrowse_script.sh
 RUN rm -rf ./node_modules
+RUN ls -alh
 
 # Stage 2: Load into nginx
 FROM nginx:alpine
 
 WORKDIR /usr/share/nginx/html
 RUN rm -rf ./*
-COPY --from=jbrowse_builder /app/annelids/ .
+COPY --from=jbrowse_builder /app/ .
 ENTRYPOINT ["nginx", "-g", "daemon off;"]

image/jbrowse_script.sh

 #!/bin/bash -eux
 # Platy only for now
+jbrowse create annelids
+cd annelids
 jbrowse add-assembly https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz --name pdumv021
 jbrowse add-track https://s3.embl.de/annelids/pdumv021/pdumv021.sorted.gff.gz -d "Kevin pdumv021 GTF file" -n "Genes models" --category "Annotations"
 jbrowse add-track https://s3.embl.de/annelids/pdumv021/transdecoder.gff.gz -d "Kevin runs transdecoder" -n "Transdecoder results" --category "Annotations"