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Commit cd9116f2 authored by cyril.cros's avatar cyril.cros
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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
parent b5ca31f5
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......@@ -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
......
# 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 ./*
......
#!/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
......
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