will try soon to build the image

TODO.md

 # TODO
 
 - use htslib for bgzip and tabix
+- npx @jbrowse/cli add-assembly https://s3.embl.de/annelids/pdumv021_genome.fa.gz --name pdumv021
 - use SAMtools for faidx
\ No newline at end of file

image/Dockerfile

+# Stage 1: Jbrowse config file generated
+FROM quay.io/biocontainers/jbrowse2:2.10.2--h5284365_0 as jbrowse_builder
+
+WORKDIR /app
+RUN jbrowse create annelids && cd annelids
+COPY jbrowse_script.sh .
+RUN ./jbrowse_script.sh
+RUN rm -rf ./node_modules
+
+# Stage 2: 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;"]

image/jbrowse_script.sh

+#!/bin/bash -eux
+# Platy only for now
+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"