Check docker

.gitlab-ci.yml

@@ -2,26 +2,46 @@
 variables:
   S3_ENDPOINT: "https://s3.embl.de"
   S3_BUCKET: "annelids"
+  JBROWSE_HOSTNAME: "genomes.arendt.embl.de"
+
 stages:
-  - upload_to_s3
+  - access_test
+  - build_container
   - deploy_to_cluster
   - clean_up_on_failure
+
 s3_access_test:
   image: minio/mc
-  stage: upload_to_s3
+  stage: access_test
+  rules:
+    - changes: # TODO change where necessary
+      - image/*
   before_script:
     - mc alias set genomes $S3_ENDPOINT $S3_ACCESS_KEY $S3_SECRET_KEY
   script:
     - mc ls genomes/$S3_BUCKET
+    - cd image
+
 cluster_access_test:
   image: dtzar/helm-kubectl:3.8.2
-  stage: deploy_to_cluster
+  stage: access_test
   before_script:
     - cd deployment
     - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
     - export KUBECONFIG=/tmp/kubeconf
   script:
     - kubectl config current-context
+
+build_nginx_with_jbrowse_config_file:
+  image: gcr.io/kaniko-project/executor:debug-v0.21.0
+  stage: build_container
+  before_script:
+    - echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
+  script:
+    - /kaniko/executor --cache=true --context $CI_PROJECT_DIR/image 
+      --dockerfile $CI_PROJECT_DIR/image/Dockerfile 
+      --destination $CI_REGISTRY_IMAGE:jbrowse2-$CI_COMMIT_SHORT_SHA
+
 kustomize_build_apply:
   image: dtzar/helm-kubectl:3.8.2
   stage: deploy_to_cluster
@@ -29,10 +49,13 @@ kustomize_build_apply:
     - echo $KUBECONFIG | base64 -d > /tmp/kubeconf
     - export KUBECONFIG=/tmp/kubeconf
   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
+    - kubectl -n $NS rollout status deployment/jbrowse2
   dependencies:
     - cluster_access_test
+
 clean_up_k8s_deployment:
   image: dtzar/helm-kubectl:3.8.2
   stage: clean_up_on_failure
@@ -42,4 +65,5 @@ clean_up_k8s_deployment:
     - export KUBECONFIG=/tmp/kubeconf
   script:
     - echo 'Failed job, deleting resources'
-    - kubectl delete -k deployment 
\ No newline at end of file
+    - envsubst < deployment/jbrowse2-dep.tmpl > deployment/jbrowse2-dep.yaml
+    - kubectl delete -k deployment

TODO.md

 # TODO
 
 - use htslib for bgzip and tabix
+- npx @jbrowse/cli add-assembly https://s3.embl.de/annelids/pdumv021_genome.fa.gz --name pdumv021
 - use SAMtools for faidx
\ 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:
@@ -16,9 +16,11 @@ spec:
       labels:
         app: jbrowse2
     spec:
+      imagePullSecrets:
+        - name: gitlab-token-auth 
       containers:
         - name: jbrowse2
-          image: nginx:alpine
+          image: ${CI_REGISTRY_IMAGE}:jbrowse2-${CI_COMMIT_SHORT_SHA}
           imagePullPolicy: Always
           resources:
             requests:
@@ -36,7 +38,7 @@ apiVersion: v1
 kind: Service
 metadata:
   name: jbrowse2
-  namespace: jbrowse2-platy
+  namespace: ${NS}
 spec:
   selector:
     app: jbrowse2
@@ -50,13 +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: /
@@ -68,4 +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

image/Dockerfile

+# Stage 1: Jbrowse config file generated
+FROM quay.io/biocontainers/jbrowse2:2.10.2--h5284365_0 as jbrowse_builder
+
+WORKDIR /app
+COPY jbrowse_script.sh .
+RUN ./jbrowse_script.sh
+RUN rm -rf annelids/node_modules
+
+# Stage 2: Load into nginx
+FROM nginx:alpine
+
+WORKDIR /usr/share/nginx/html
+RUN rm -rf ./*
+COPY --from=jbrowse_builder /app/annelids/ .
+ENTRYPOINT ["nginx", "-g", "daemon off;"]

image/jbrowse_script.sh

+#!/bin/bash -eux
+# Platy only for now
+jbrowse create annelids
+cd annelids
+jbrowse add-assembly https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz --name pdumv021
+jbrowse add-track https://s3.embl.de/annelids/pdumv021/pdumv021.gff.gz -d "Kevin pdumv021 GTF file" -n "Genes models" --category "Annotations"
+jbrowse add-track https://s3.embl.de/annelids/pdumv021/transdecoder.gff.gz -d "Kevin runs transdecoder" -n "Transdecoder results" --category "Annotations"