Let's see how this goes now 6

.gitlab-ci.yml

@@ -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

deployment/jbrowse2-dep.yaml → deployment/jbrowse2-dep.tmpl

@@ -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