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Commit 40dd7072 authored by cyril.cros's avatar cyril.cros
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will try soon to build the image

parent 697f9de3
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Tags v0.0.1
1 merge request!1Check docker
Pipeline #58297 canceled
# 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
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# 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;"]
#!/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"
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