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Jbrowse2 Annelids
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Arendt Group
Jbrowse2 Annelids
Commits
11334d39
Commit
11334d39
authored
10 months ago
by
cyril.cros
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Let's see how this goes now 6
parent
8f77ee79
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Pipeline
#58321
failed
10 months ago
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2 changed files
.gitlab-ci.yml
+16
-14
16 additions, 14 deletions
.gitlab-ci.yml
deployment/jbrowse2-dep.tmpl
+7
-7
7 additions, 7 deletions
deployment/jbrowse2-dep.tmpl
with
23 additions
and
21 deletions
.gitlab-ci.yml
+
16
−
14
View file @
11334d39
...
...
@@ -2,17 +2,17 @@
variables
:
S3_ENDPOINT
:
"
https://s3.embl.de"
S3_BUCKET
:
"
annelids"
JBROWSE_HOSTNAME
:
"
genomes.arendt.embl.de"
stages
:
-
download_from_s3
-
upload_to_s3
-
access_test
-
build_container
-
deploy_to_cluster
-
clean_up_on_failure
s3_access_test
:
image
:
minio/mc
stage
:
download_from_s3
stage
:
access_test
rules
:
-
changes
:
# TODO change where necessary
-
image/*
...
...
@@ -22,6 +22,16 @@ s3_access_test:
-
mc ls genomes/$S3_BUCKET
-
cd image
cluster_access_test
:
image
:
dtzar/helm-kubectl:3.8.2
stage
:
access_test
before_script
:
-
cd deployment
-
echo $KUBECONFIG | base64 -d > /tmp/kubeconf
-
export KUBECONFIG=/tmp/kubeconf
script
:
-
kubectl config current-context
build_nginx_with_jbrowse_config_file
:
image
:
gcr.io/kaniko-project/executor:debug-v0.21.0
stage
:
build_container
...
...
@@ -32,28 +42,19 @@ build_nginx_with_jbrowse_config_file:
--dockerfile $CI_PROJECT_DIR/image/Dockerfile
--destination $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
cluster_access_test
:
image
:
dtzar/helm-kubectl:3.8.2
stage
:
deploy_to_cluster
before_script
:
-
cd deployment
-
echo $KUBECONFIG | base64 -d > /tmp/kubeconf
-
export KUBECONFIG=/tmp/kubeconf
script
:
-
kubectl config current-context
kustomize_build_apply
:
image
:
dtzar/helm-kubectl:3.8.2
stage
:
deploy_to_cluster
before_script
:
-
echo $KUBECONFIG | base64 -d > /tmp/kubeconf
-
export KUBECONFIG=/tmp/kubeconf
-
kubectl -n $NS create --dry-run=client -o yaml
-
kubectl -n $NS create --dry-run=client -o yaml
--save-config=true
# secret
secret docker-registry gitlab-auth-token
--docker-server=$CI_REGISTRY --docker-username=$CI_REGISTRY_USER
--docker-password=$CI_REGISTRY_PASSWORD |
kubectl apply -f -
script
:
-
envsubst < deployment/jbrowse2-dep.tmpl > deployment/jbrowse2-dep.yaml
-
kubectl apply -k deployment
-
kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2
dependencies
:
...
...
@@ -68,5 +69,6 @@ clean_up_k8s_deployment:
-
export KUBECONFIG=/tmp/kubeconf
script
:
-
echo 'Failed job, deleting resources'
-
envsubst < deployment/jbrowse2-dep.tmpl > deployment/jbrowse2-dep.yaml
-
kubectl delete -k deployment
-
kubectl -n $NS delete secret gitlab-auth-token
\ No newline at end of file
This diff is collapsed.
Click to expand it.
deployment/jbrowse2-dep.
yam
l
→
deployment/jbrowse2-dep.
tmp
l
+
7
−
7
View file @
11334d39
...
...
@@ -3,7 +3,7 @@ apiVersion: apps/v1
kind: Deployment
metadata:
name: jbrowse2
namespace
:
jbrowse2-platy
namespace:
${NS}
labels:
name: jbrowse2
spec:
...
...
@@ -17,10 +17,10 @@ spec:
app: jbrowse2
spec:
imagePullSecrets:
-
gitlab-token-auth
-
name:
gitlab-token-auth
containers:
- name: jbrowse2
image
:
image:
${CI_REGISTRY_IMAGE}:jbrowse2-${CI_COMMIT_SHORT_SHA}
imagePullPolicy: Always
resources:
requests:
...
...
@@ -38,7 +38,7 @@ apiVersion: v1
kind: Service
metadata:
name: jbrowse2
namespace
:
jbrowse2-platy
namespace:
${NS}
spec:
selector:
app: jbrowse2
...
...
@@ -52,13 +52,13 @@ apiVersion: networking.k8s.io/v1
kind: Ingress
metadata:
name: jbrowse2
namespace
:
jbrowse2-platy
namespace:
${NS}
annotations:
traefik.ingress.kubernetes.io/router.tls.certresolver: sectigo
spec:
ingressClassName: external-users
rules:
-
host
:
genomes.arendt.embl.de
- host:
${JBROWSE_HOSTNAME}
http:
paths:
- path: /
...
...
@@ -70,4 +70,4 @@ spec:
name: http
tls:
- hosts:
-
genomes.arendt.embl.de
\ No newline at end of file
- ${JBROWSE_HOSTNAME}
\ No newline at end of file
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