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Commit 079b550e authored by cyril.cros's avatar cyril.cros
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More CI/CD

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Pipeline #58238 failed
--- ---
variables:
- S3_ENDPOINT: https://s3.embl.de
- S3_BUCKET: annelids
stages: stages:
- upload_to_s3
- deploy_to_cluster - deploy_to_cluster
- clean_up_on_failure - 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: cluster_access_test:
image: dtzar/helm-kubectl:3.8.2 image: dtzar/helm-kubectl:3.8.2
stage: deploy_to_cluster stage: deploy_to_cluster
script: before_script:
- cd deployment - cd deployment
- echo $KUBECONFIG | base64 -d > /tmp/kubeconf - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
- export KUBECONFIG=/tmp/kubeconf - export KUBECONFIG=/tmp/kubeconf
script:
- kubectl config current-context - kubectl config current-context
kustomize_build_apply: kustomize_build_apply:
image: dtzar/helm-kubectl:3.8.2 image: dtzar/helm-kubectl:3.8.2
stage: deploy_to_cluster stage: deploy_to_cluster
script: before_script:
- echo $KUBECONFIG | base64 -d > /tmp/kubeconf - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
- export KUBECONFIG=/tmp/kubeconf - export KUBECONFIG=/tmp/kubeconf
script:
- kubectl apply -k deployment - kubectl apply -k deployment
- kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2 - kubectl -n $NS wait --for=condition=available --timeout=60s deploy/jbrowse2
dependencies: dependencies:
...@@ -24,8 +37,9 @@ clean_up_k8s_deployment: ...@@ -24,8 +37,9 @@ clean_up_k8s_deployment:
image: dtzar/helm-kubectl:3.8.2 image: dtzar/helm-kubectl:3.8.2
stage: clean_up_on_failure stage: clean_up_on_failure
when: on_failure when: on_failure
script: before_script:
- echo 'Failed job, deleting resources'
- echo $KUBECONFIG | base64 -d > /tmp/kubeconf - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
- export KUBECONFIG=/tmp/kubeconf - export KUBECONFIG=/tmp/kubeconf
script:
- echo 'Failed job, deleting resources'
- kubectl delete -k deployment - 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
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