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Jbrowse2 Annelids
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Arendt Group
Jbrowse2 Annelids
Commits
079b550e
Commit
079b550e
authored
10 months ago
by
cyril.cros
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parent
31803e1a
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Pipeline
#58238
failed
10 months ago
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.gitlab-ci.yml
+18
-4
18 additions, 4 deletions
.gitlab-ci.yml
TODO.md
+4
-0
4 additions, 0 deletions
TODO.md
with
22 additions
and
4 deletions
.gitlab-ci.yml
+
18
−
4
View file @
079b550e
---
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
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TODO.md
0 → 100644
+
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−
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079b550e
# TODO
-
use htslib for bgzip and tabix
-
use SAMtools for faidx
\ No newline at end of file
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