More CI/CD

.gitlab-ci.yml

 ---
+variables:
+  - S3_ENDPOINT: https://s3.embl.de
+  - S3_BUCKET: annelids
 stages:
+  - upload_to_s3
   - deploy_to_cluster
   - clean_up_on_failure
+s3_access_test:
+  image: minio/mc
+  stage: upload_to_s3
+  before_script:
+    - mc alias set genomes $S3_ENDPOINT $S3_ACCESS_KEY $S3_SECRET_KEY
+  script:
+    - mc ls genomes/$S3_BUCKET
 cluster_access_test:
   image: dtzar/helm-kubectl:3.8.2
   stage: deploy_to_cluster
-  script:
+  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
-  script:
+  before_script:
     - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
     - export KUBECONFIG=/tmp/kubeconf
+  script:
     - kubectl apply -k deployment
     - kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2
   dependencies:
@@ -24,8 +37,9 @@ clean_up_k8s_deployment:
   image: dtzar/helm-kubectl:3.8.2
   stage: clean_up_on_failure
   when: on_failure
-  script:
-    - echo 'Failed job, deleting resources'
+  before_script:
     - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
     - export KUBECONFIG=/tmp/kubeconf
+  script:
+    - echo 'Failed job, deleting resources'
     - kubectl delete -k deployment 
\ No newline at end of file

TODO.md

+# TODO
+
+- use htslib for bgzip and tabix
+- use SAMtools for faidx
\ No newline at end of file