Skip to content
Snippets Groups Projects
Commit 079b550e authored by cyril.cros's avatar cyril.cros
Browse files

More CI/CD

parent 31803e1a
No related branches found
No related tags found
No related merge requests found
Pipeline #58238 failed
---
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
- use htslib for bgzip and tabix
- use SAMtools for faidx
\ No newline at end of file
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment