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Arendt Group
Jbrowse2 Annelids
Commits
ef09e064
Commit
ef09e064
authored
5 months ago
by
cyril.cros
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Fix config.json issues
parent
5a73bac5
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Pipeline
#65767
failed
5 months ago
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2 changed files
.gitlab-ci.yml
+0
-8
0 additions, 8 deletions
.gitlab-ci.yml
image/Dockerfile
+6
-4
6 additions, 4 deletions
image/Dockerfile
with
6 additions
and
12 deletions
.gitlab-ci.yml
+
0
−
8
View file @
ef09e064
...
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@@ -47,14 +47,6 @@ build_nginx_with_jbrowse_config_file:
-
echo "Destination follows"
-
echo $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
show_me_my_config
:
stage
:
deploy
image
:
$CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
needs
:
-
build_nginx_with_jbrowse_config_file
script
:
-
cat /usr/share/nginx/html/config.json
deploy_to_k8s
:
stage
:
deploy
image
:
dtzar/helm-kubectl:3.8.2
...
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image/Dockerfile
+
6
−
4
View file @
ef09e064
...
...
@@ -4,11 +4,13 @@ FROM ghcr.io/jqlang/jq:1.7.1 as jq
# Stage 1: Jbrowse config file generated
FROM
quay.io/biocontainers/jbrowse2:2.15.3--hbbc3ce4_0
as
jbrowse_builder
WORKDIR
/app/annelids
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
\
COPY
jbrowse_script_base.sh ./
RUN
./jbrowse_script_base.sh
COPY
tracks.json default_session.json ./
RUN
./jq
--rawfile
base default_session.json
'.defaultSession = $base'
config.json
>
config_tmp.json
\
&&
./jq
--rawfile
base tracks.json
'. += $base'
config_tmp.json
>
config_final.json
\
&&
mv
config_final.json config.json
\
&&
rm
-rf
node_modules jq jbrowse_script_base.sh default_session.json tracks.json
# Stage 2: Load into nginx
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