values.yaml

# Default values for Galaxy.
# Declare variables to be passed into your templates.

#- Partial override of the `galaxy.fullname`.  The `.Release.Name` will be prepended to generate the fullname.
nameOverride: ""
#- Fully override the `galaxy.fullname`
fullnameOverride: ""

image:
  #- Repository containing the Galaxy image.
  repository: quay.io/galaxyproject/galaxy-min
  #- Galaxy Docker image tag (generally corresponds to the desired Galaxy version)
  tag: "24.1.1"  # Galaxy versions prior to 24.1.1 contain a bug mapping the extra_files directory
  #-  Galaxy image [pull policy](https://kubernetes.io/docs/concepts/configuration/overview/#container-images)
  pullPolicy: IfNotPresent

#- Secrets used to [access a Galaxy image from a private repository](https://kubernetes.io/docs/tasks/configure-pod-container/pull-image-private-registry/)
imagePullSecrets: []

trainingHook:
  #- Enable the GTN webhook to link references to tools in tutorials to the corresponding tool panel in Galaxy.
  enabled: false
  #- The training material server used to service the training-material webhook.
  url: https://training.galaxyproject.org/training-material/

service:
  #- The Galaxy service type
  type: ClusterIP
  #- The port Galaxy is listening to
  port: 8000
  #- The external port exposed on each node
  nodePort: 30700

workflowHandlers:
  replicaCount: 1
  startupDelay: 10 # used to avoid race conditions
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  startupProbe:
    enabled: true
    initialDelaySeconds: 30
    periodSeconds: 5
    failureThreshold: 80
    timeoutSeconds: 5
  readinessProbe:
    enabled: true
    periodSeconds: 10
    failureThreshold: 12
    timeoutSeconds: 5
  livenessProbe:
    enabled: true
    periodSeconds: 10
    failureThreshold: 30
    timeoutSeconds: 5

webHandlers:
  replicaCount: 1
  startupDelay: 0 # used to avoid race conditions
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  startupProbe:
    enabled: true
    initialDelaySeconds: 30
    periodSeconds: 5
    failureThreshold: 80
    timeoutSeconds: 5
  readinessProbe:
    enabled: true
    periodSeconds: 10
    failureThreshold: 12
    timeoutSeconds: 5
  livenessProbe:
    enabled: true
    periodSeconds: 10
    failureThreshold: 30
    timeoutSeconds: 5
  gunicorn:
    timeout: 300
    workers: 1
    extraArgs: ""

jobHandlers:
  replicaCount: 1
  startupDelay: 5 # used to avoid race conditions
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  startupProbe:
    enabled: true
    initialDelaySeconds: 30
    periodSeconds: 5
    failureThreshold: 80
    timeoutSeconds: 5
  readinessProbe:
    enabled: true
    periodSeconds: 10
    failureThreshold: 12
    timeoutSeconds: 5
  livenessProbe:
    enabled: true
    periodSeconds: 10
    failureThreshold: 30
    timeoutSeconds: 5

celery:
  concurrency: 2
  logLevel: "INFO"
  extraArgs: ""
  replicaCount: 1
  startupDelay: 5 # used to avoid race conditions
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  startupProbe:
    enabled: false
    initialDelaySeconds: 15
    periodSeconds: 60
    failureThreshold: 40
    timeoutSeconds: 10
  readinessProbe:
    enabled: false
    periodSeconds: 60
    failureThreshold: 12
    timeoutSeconds: 10
  livenessProbe:
    enabled: false
    periodSeconds: 60
    failureThreshold: 30
    timeoutSeconds: 10

celeryBeat:
  logLevel: "INFO"
  extraArgs: ""
  replicaCount: 1
  startupDelay: 5 # used to avoid race conditions
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  startupProbe:
    enabled: false
    initialDelaySeconds: 15
    periodSeconds: 60
    failureThreshold: 40
    timeoutSeconds: 10
  readinessProbe:
    enabled: false
    periodSeconds: 60
    failureThreshold: 12
    timeoutSeconds: 10
  livenessProbe:
    enabled: false
    periodSeconds: 60
    failureThreshold: 30
    timeoutSeconds: 10

metrics:
  #- Enable the metrics server. Defaults to `false`
  enabled: false
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  image:
    repository: cloudve/galaxy-metrics-scraper
    tag: 2.1.0
    pullPolicy: IfNotPresent

serviceAccount:
  #- Specifies whether a service account should be created
  create: true
  #- Annotations to add to the service account
  annotations: {}
  #- The name of the service account to use.
  #- If not set and create is true, a name is generated using the fullname template
  name: ""

rbac:
  #- Does the cluster use role based access control.
  enabled: true

securityContext:
  #- Security context and file system group used by jobs.
  fsGroup: 101

#- Configure the PVC used by Galaxy for local storage.
persistence:
  #- Persistence is enabled by default
  enabled: true
  #- Name of the PVC to create
  name: galaxy-pvc
  annotations: {}
  #- StorageClass for the PVC. Must support `ReadWriteMany`.
  storageClass: ""
  #- The name of an existing PVC to use for persistence.
  existingClaim: null
  accessMode: ReadWriteMany
  size: 5Gi
  mountPath: /galaxy/server/database

extraVolumes: []
#   - name: shared-data
#     persistentVolumeClaim:
#       claimName: shared-data-pvc

extraVolumeMounts: []
#   - name: shared-data
#     mountPath: /mnt/project/shared-data

#- tasks to perform once after installation
setupJob:
  #- create the database
  createDatabase: true
  securityContext:
    #- the setup jobs will run as this user
    runAsUser: 101
    #- the `runAsUser` will belong to this group.
    runAsGroup: 101
    #- the filesystem group
    fsGroup: 101
  ttlSecondsAfterFinished: 300
  downloadToolConfs:
    enabled: true
    # Uses Galaxy's shared file system volume
    volume:
      subPath: cvmfsclone # on galaxy-data volume (avoid config, tools, lib, etc...)
      mountPath: /cvmfs/cloud.galaxyproject.org
    archives:
      #- A tar.gz publicly accessible archive containing AT LEAST conf files and XML tool wrappers.
      #- Meant to be enough for Galaxy handlers to startup
      startup: https://storage.googleapis.com/cloud-cvmfs/startup.tar.gz
      #- A tar.gz publicly accessible archive containing AT LEAST confs, tool wrappers, and scripts
      #- excluding test data.
      #- Meant to be enough for Galaxy handlers to run jobs.
      running: https://storage.googleapis.com/cloud-cvmfs/partial.tar.gz
      #- A tar.gz publicly accessible archive containing the full `tools` directory,
      #- including each tool's test data.
      #- Meant to be enough to run automated tool-tests, fully mimicking CVMFS setup
      full: https://storage.googleapis.com/cloud-cvmfs/contents.tar.gz

#- Allow users to specify extra init containers
extraInitContainers: []
#   - name: my-first-container
#     applyToJob: true
#     applyToWeb: true
#     applyToWorkflow: true
#     image: "{{.Values.image.repository}}:{{.Values.image.tag}}"
#     args: ['sh', '-c', 'cp "/galaxy/server/config/job_conf.xml.sample_advanced" {{.Values.persistence.mountPath}}/']
#     volumeMounts:
#       - name: galaxy-data
#         mountPath: "{{.Values.persistence.mountPath}}"
#   - name: my-second-container
#     applyToJob: true
#     applyToWeb: false
#     applyToWorkflow: true
#     image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
#     args: ['sh', '-c', 'cp "/galaxy/server/config/galaxy.yml" {{.Values.persistence.mountPath}}/']
#     volumeMounts:
#       - name: galaxy-data
#         mountPath: "{{.Values.persistence.mountPath}}"

extraInitCommands: ""
#  echo "Running extra mapped script. Influx enabled = {{ .Values.influxdb.enabled }}";
#  /galaxy/server/extra/mapped/script.sh

extraEnv: []
  # - name: EXAMPLE_ENV
  #   value: MY_VALUE

#- CronJobs to perform periodic maintenance tasks
cronJobs:
  #- Runs the maintenance.sh script to purge items in the Galaxy database that
  #- have been flagged as deleted.
  maintenance:
    enabled: true
    schedule: "5 2 * * *"
    extraSettings:
      #- Purge items older than this.
      days: '7'
    securityContext:
      runAsUser: 0
    defaultEnv: true
    command:
      - "/galaxy/server/scripts/maintenance.sh"
    args:
      - "--no-dry-run"
      - "--days"
      - "{{ tpl .Values.cronJobs.maintenance.extraSettings.days $ }}"
  #- Remove files from the tmp directory that are older than the allowable wall time for a job
  tmpdir:
    enabled: true
    schedule: "15 2 * * *"
    extraSettings:
      lastModified: '{{ index .Values "configs" "job_conf.yml" "runners" "k8s" "k8s_walltime_limit" | default 604800 }}'
    securityContext:
      runAsUser: 0
    command:
      - /usr/bin/find
    args:
      - "{{ .Values.persistence.mountPath }}/tmp"
      - "!"
      - "-newermt"
      - "{{ tpl .Values.cronJobs.tmpdir.extraSettings.lastModified $ }} seconds ago"
      - "-type"
      - "f"
      - "-exec"
      - "rm"
      - "{}"
      - ";"
#  #- An example cron job that showcases all available features.
#  example:
#    #- Disable the job by scheduling it for a date that never occurs, I.E. Feb 30th
#    #- The job can still be triggered manually.
#    schedule: "0 0 30 2 *"
#    #- Include the set of default environment variables. See galaxy.podEnvVars
#    #- in the Helm chart's _helpers.tpl for the variables that will be defined.
#    defaultEnv: true
#    #- Define extra environment variables that will be available to the job
#    extraEnv:
#      - name: LOGFILE
#        value: /galaxy/server/database/example.log
#    #- Run the job as root (uid 0)
#    securityContext:
#      runAsUser: 0
#    #- Specify an alternate Docker image for the CronJob container
#    image:
#      repository: ksuderman/galaxy-maintenance
#      tag: "0.7"
#    #- The command to be run
#    command:
#      - /usr/local/bin/example.sh
#    #- Command line arguments to be passed to the command, one per line.
#    args:
#      - "--option"
#      - "value"
#    #- Define extra files that will be mounted into the image. In this case we
#    #- mount a simple Bash script that will write the current environment
#    #- variables to persistent storage.
#    extraFileMappings:
#      #- Path were the file will be mounted
#      /usr/local/bin/example.sh:
#        #- Default permission on the file.  In this case 'rwxr-xr-x'
#        mode: "0755"
#        #- Run the contents through the Helm `tpl` command
#        tpl: true
#        #- The contents of the file to be mounted.  Can contain Helm template values
#        #- if `tpl` is set to true.
#        content: |-
#          #!/usr/bin/bash
#          echo {{ .Release.Name }} >> $LOGFILE
#          echo "$@" >> $LOGFILE
#          env >> $LOGFILE

ingress:
  #- Should ingress be enabled. Defaults to `true`
  enabled: true
  ingressClassName: nginx
  canary:
    enabled: true
  annotations:
    nginx.ingress.kubernetes.io/proxy-body-size: "10G"
    nginx.ingress.kubernetes.io/proxy-read-timeout: "600"
    # kubernetes.io/ingress.class: nginx
    # kubernetes.io/tls-acme: "true"
  path: /galaxy
  hosts:
    - host: ~
      paths:
        - path: "/galaxy"
        - path: "/training-material"
  tls: []
  #  - secretName: chart-example-tls
  #    hosts:
  #      - chart-example.local

resources:
  #- We recommend updating these based on the usage levels of the server.
  requests:
    cpu: 100m
    memory: 1G
    ephemeral-storage: 1Gi
  limits:
    cpu: 3
    memory: 7G
    ephemeral-storage: 10Gi

nodeSelector: {}

tolerations: []

affinity: {}

postgresql:
  enabled: true
  #- Whether to deploy the postgresl operator.
  #- In general, we recommend installing the operator globally in production.
  deploy: true
  #- hostname and port of an existing database to use.
  existingDatabase:
  galaxyDatabaseUser: galaxydbuser
  galaxyConnectionParams: "?sslmode=require"
  # Password is autogenerated and stored in a secret if not specified
  # galaxyDatabasePassword:
  # galaxyExistingSecret:
  # galaxyExistingSecretKeyRef:
  operator:
    operatorSpecExtra:
  nameOverride: postgres
  persistence:
    enabled: true
    #storageClass:
    #size:
    #extra:
    #  selector:
    #    matchLabels:
    #      label-key: label-value

#- Configuration block for reference data
refdata:
  #- Whether or not to mount cloud-hosted Galaxy reference data and tools.
  enabled: true
  #- `s3csi` or `cvmfs`, determines the CSI to use for mounting reference data.
  #-`cvmfs` is the default and recommended for the time being.
  type: cvmfs
  pvc:
    size: 10Gi

#- Configuration block if `cvmfs` is used as `refdata.type`
cvmfs:
  #- Deploy the Galaxy-CVMFS-CSI Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource
  deploy: true
  #- Deploy the CVMF post install fix,
  deployPostInstallFix: true
  storageClassName: "{{ $.Release.Name }}-cvmfs"
  cvmfscsi:
    cache:
      alien:
        pvc:
          name: cvmfs-alien-cache

#- Configuration block if `s3csi` is used as the `refdata.type`
s3csi:
  #- Deploy the CSI-S3 Helm Chart. This is an optional dependency, and for production scenarios it should be deployed separately as a cluster-wide resource.
  deploy: false
  images:
    csi: cloudve/csi-s3:0.31.3
  storageClass:
    name: refdata-gxy-data
    mounter: s3fs
    singleBucket: biorefdata
    mountOptions: "-o use_cache=/tmp -o endpoint=ap-southeast-2 -o public_bucket=1 -o enable_noobj_cache -o no_check_certificate -o kernel_cache -o ensure_diskfree=5000"
    # additional optimizations for s3fs
    # -o max_background=1000 -o max_stat_cache_size=1000000 -o multipart_size=52 -o parallel_count=30 -o multireq_max=30 -o dbglevel=warn
    # future settings for geesefs
    # mountOptions: "--memory-limit 4000 --dir-mode 0777 --file-mode 0666 --cache /tmp/geesecache --debug --debug_fuse --stat-cache-ttl 9m0s --cache-to-disk-hits 1"
    # --no-dir-object --no-implicit-dir --stat-cache-ttl 120m0s --max-disk-cache-fd 4096
  secret:
    endpoint: https://s3.ap-southeast-2.amazonaws.com
    usePrefix: true
    prefix: /galaxy/v1/data.galaxyproject.org

#- When this flag is set to true, all configs will be set in secrets,
#- when it is set to false, all configs will be set in configmaps
useSecretConfigs: false

#- All config files will be relative to `/galaxy/server/config/` directory
configs:
  job_conf.yml:
    runners:
      local:
        load: galaxy.jobs.runners.local:LocalJobRunner
        workers: 4
      k8s:
        load: galaxy.jobs.runners.kubernetes:KubernetesJobRunner
        k8s_use_service_account: true
        k8s_data_volume_claim: |-
          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
        k8s_working_volume_claim: |-
          {{ template "galaxy.pvcname" . -}}:{{ .Values.persistence.mountPath -}}
        k8s_persistent_volume_claims: |-
          {{ template "galaxy.pvcname" . -}}/config:{{ .Values.persistence.mountPath -}}/config:r,
          {{- template "galaxy.pvcname" . -}}/tmp:{{ .Values.persistence.mountPath -}}/tmp:rw,
          {{- template "galaxy.pvcname" . -}}/tool-data:{{ .Values.persistence.mountPath -}}/tool-data:rw,
          {{- template "galaxy.pvcname" . -}}/tools:{{ .Values.persistence.mountPath -}}/tools:r,
          {{- template "galaxy.pvcname" . -}}/shed_tools:{{ .Values.persistence.mountPath -}}/shed_tools:r
          {{- if .Values.refdata.enabled -}}
          {{- if eq .Values.refdata.type "cvmfs" -}}
          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc/data.galaxyproject.org:/cvmfs/data.galaxyproject.org:r
          {{- else -}}
          ,{{- template "galaxy.fullname" $ -}}-refdata-gxy-pvc:/cvmfs/data.galaxyproject.org:r
          {{- end -}}
          {{- end -}}
          {{- if .Values.setupJob.downloadToolConfs.enabled -}}
          ,{{ template "galaxy.pvcname" . -}}/{{ .Values.setupJob.downloadToolConfs.volume.subPath }}:{{ .Values.setupJob.downloadToolConfs.volume.mountPath -}}:r
          {{- end -}}
          {{- if .Values.extraVolumes -}}
          {{- template "galaxy.extra_pvc_mounts" . -}}
          {{- end }}
        k8s_namespace: "{{ .Release.Namespace }}"
        k8s_galaxy_instance_id: "{{ .Release.Name }}"
        k8s_fs_group_id: "101"
        k8s_supplemental_group_id: "101"
        k8s_pull_policy: IfNotPresent
        k8s_cleanup_job: onsuccess
        k8s_job_ttl_secs_after_finished: 90
        k8s_pod_priority_class: >-
          {{ if .Values.jobs.priorityClass.enabled -}}
            {{- include "galaxy.pod-priority-class" . }}
          {{- end }}
        k8s_interactivetools_use_ssl: true
        k8s_interactivetools_ingress_annotations: |
          {{.Values.ingress.annotations | toYaml | nindent 6 }}
    handling:
      assign:
        - "db-skip-locked"
    execution:
      default: tpv_dispatcher
      environments:
        tpv_dispatcher:
          container_monitor: false
          runner: dynamic
          type: python
          function: map_tool_to_destination
          rules_module: tpv.rules
          docker_default_container_id: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
          tpv_config_files:
            - https://gxy.io/tpv/db.yml
            - lib/galaxy/jobs/rules/tpv_rules_local.yml
#     limits:
#     - type: registered_user_concurrent_jobs
#       value: 5
#     - type: anonymous_user_concurrent_jobs
#       value: 2

  #- Galaxy configuration. See the [Galaxy documentation](https://docs.galaxyproject.org/en/master/admin/config.html)
  #- for more information.
  galaxy.yml:
    galaxy:
      galaxy_url_prefix: "{{ .Values.ingress.path }}"
      interactivetools_enable: true
      interactivetools_map: database/interactivetools_map.sqlite
      interactivetools_prefix: "its"
      interactivetools_proxy_host: '{{ $host := index .Values.ingress.hosts 0 }}{{ default "localhost" $host.host}}'
      interactivetools_shorten_url: true
      interactivetools_base_path: "{{$host := index .Values.ingress.hosts 0}}{{$path := index $host.paths 0}}{{$path.path}}"
      id_secret:
      mulled_resolution_cache_lock_dir: "/galaxy/server/local/mulled_cache_lock"
      database_connection: |-
        {{ include "galaxy-postgresql.connection-string" .}}
      integrated_tool_panel_config: "/galaxy/server/config/mutable/integrated_tool_panel.xml"
      sanitize_allowlist_file: "/galaxy/server/config/mutable/sanitize_allowlist.txt"
      tool_config_file: "/galaxy/server/config/tool_conf.xml{{if .Values.setupJob.downloadToolConfs.enabled}},{{ .Values.setupJob.downloadToolConfs.volume.mountPath }}/config/shed_tool_conf.xml{{end}}"
      shed_tool_config_file: "/galaxy/server/config/mutable/editable_shed_tool_conf.xml"
      enable_tool_document_cache: false
      tool_data_table_config_path: |-
        {{ if .Values.setupJob.downloadToolConfs.enabled }}
        {{- .Values.setupJob.downloadToolConfs.volume.mountPath }}/config/shed_tool_data_table_conf.xml
        {{- if .Values.refdata.enabled -}}
        ,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml
        {{- end }}
        {{- else }}
        {{- if .Values.refdata.enabled -}}
        /cvmfs/data.galaxyproject.org//managed/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml
        {{- end }}
        {{- end }}
      tool_dependency_dir: "{{.Values.persistence.mountPath}}/deps"
      job_config_file: "/galaxy/server/config/job_conf.yml"
      builds_file_path: |-
        {{ if .Values.refdata.enabled }}
        /cvmfs/data.galaxyproject.org/managed/location/builds.txt
        {{- end }}
      containers_resolvers_config_file: "/galaxy/server/config/container_resolvers_conf.xml"
      workflow_schedulers_config_file: "/galaxy/server/config/workflow_schedulers_conf.xml"
      build_sites_config_file: "/galaxy/server/config/build_sites.yml"
      shed_data_manager_config_file: "/galaxy/server/config/mutable/shed_data_manager_conf.xml"
      shed_tool_data_table_config: "/galaxy/server/config/mutable/shed_tool_data_table_conf.xml"
      enable_data_manager_user_view: true
      tool_path: "{{.Values.persistence.mountPath}}/tools"
      tool_data_path: "{{.Values.persistence.mountPath}}/tool-data"
      conda_auto_init: false
      nginx_x_accel_redirect_base: >-
        {{include "galaxy.add_trailing_slash" .Values.ingress.path}}_x_accel_redirect
      len_file_path: |-
        {{ if .Values.refdata.enabled -}}
        /cvmfs/data.galaxyproject.org/managed/len/ucsc
        {{- end }}
  container_resolvers_conf.xml: |
    <containers_resolvers>
      <explicit />
      <mulled />
    </containers_resolvers>
  workflow_schedulers_conf.xml: |
    <?xml version="1.0"?>
    <workflow_schedulers default="core">
      <core id="core" />
      <handlers default="schedulers">
          <handler id="workflow_scheduler0" tags="schedulers"/>
      </handlers>
    </workflow_schedulers>
  sanitize_allowlist.txt: |
    toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff/3.7+galaxy0
    toolshed.g2.bx.psu.edu/repos/bgruening/pharmcat/pharmcat/1.3.1+galaxy0
    toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
    toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72
    toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.44+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/dexseq/dexseq/1.28.1+galaxy2
    toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.20.1+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse_to_standalone/1.16.11+galaxy1
    toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy1
    toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.11+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6
    toolshed.g2.bx.psu.edu/repos/iuc/meme_meme/meme_meme/5.0.5.0
    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.9+galaxy1
    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.8+galaxy1
    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6
    toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.5.0
    toolshed.g2.bx.psu.edu/repos/iuc/prestor_abseq3/prestor_abseq3/0.6.2+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/5.0.2+galaxy3
    toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.1.0+galaxy0
    toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3r.1
    toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2
    toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy1
    toolshed.g2.bx.psu.edu/repos/bgruening/plotly_regression_performance_plots/plotly_regression_performance_plots/0.1
    toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.2
    toolshed.g2.bx.psu.edu/repos/bgruening/plotly_parallel_coordinates_plot/plotly_parallel_coordinates_plot/0.1
  build_sites.yml:
    - type: ucsc
      file: "{{if .Values.refdata.enabled}}/cvmfs/data.galaxyproject.org/managed/location/ucsc_build_sites.txt{{else}}/galaxy/server/tool-data/shared/ucsc/ucsc_build_sites.txt.sample{{end}}"
      display: [main,archaea,ucla]
    - type: gbrowse
      file: "/galaxy/server/tool-data/shared/gbrowse/gbrowse_build_sites.txt"
      display: [wormbase,tair,modencode_worm,modencode_fly]
    - type: ensembl
      file: "/galaxy/server/tool-data/shared/ensembl/ensembl_sites.txt"
    - type: ensembl_data_url
      file: "/galaxy/server/tool-data/shared/ensembl/ensembl_sites_data_URL.txt"
    - type: igv
      file: "/galaxy/server/tool-data/shared/igv/igv_build_sites.txt.sample"
    - type: rviewer
      file: "/galaxy/server/tool-data/shared/rviewer/rviewer_build_sites.txt.sample"
  # Although this is only one line, the multi-line entry allows us to avoid wrapping
  # the entire expression in quotes, which would need to be removed in the configmap
  integrated_tool_panel.xml: |
    {{- (.Files.Get "files/configs/integrated_tool_panel.xml") }}
  tool_conf.xml: |
    {{- (.Files.Get "files/configs/tool_conf.xml") }}

#- Additional dynamic rules to map into the container.
jobs:
  init:
    #- The Docker image to use for the init containers
    image:
      repository: alpine
      tag: 3.16
      pullPolicy: IfNotPresent
  priorityClass:
    #- Assign a [priorityClass](https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/#priorityclass) to the dispatched jobs.
    enabled: true
    existingClass: ""
    value: -1000
  rules:
    tpv_rules_local.yml:
      global:
        default_inherits: default
      tools:
        default:
          params:
            container_monitor: false
            docker_default_container_id: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
            tmp_dir: "true"
          scheduling:
            reject:
              - local
              - offline
          rules:
            - id: force_default_container_for_built_in_tools
              if: |
                from galaxy.tools import GALAXY_LIB_TOOLS_UNVERSIONED
                tool.id in GALAXY_LIB_TOOLS_UNVERSIONED or "CONVERTER_" == tool.id[:10] or tool.is_datatype_converter
              params:
                docker_container_id_override: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
        Summary_Statistics1:
          params:
            docker_container_id_override: cloudve/gsummary:latest
        toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/.*:
          params:
            docker_container_id_override: cloudve/sam-fasta-dm:latest
        toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/.*:
          params:
            docker_container_id_override: cloudve/bwa-dm:latest
        toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.14.5:
          params:
            docker_container_id_override: cloudve/prokka:1.14.5
        toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/jbrowse/1.16.5+galaxy6:
          params:
            docker_container_id_override: cloudve/jbrowse:1.16.5
        sort1:
          params:
            docker_container_id_override: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
        Grouping1:
          params:
            docker_container_id_override: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
      destinations:
        k8s:
          runner: k8s
          params:
            docker_enabled: "true"
            requests_cpu: "{cores}"
            requests_memory: "{mem}Gi"
            limits_cpu: "{cores}"
            limits_memory: "{mem}Gi"
          scheduling:
            accept:
              - docker
        local:
          runner: local
          scheduling:
            require:
              - local

extraFileMappings:
  /galaxy/server/static/welcome.html:
    useSecret: false
    applyToJob: false
    applyToWeb: true
    applyToSetupJob: false
    applyToWorkflow: false
    applyToNginx: true
    tpl: true
    content: |
      <!DOCTYPE html>
      <html lang="en">
          <head>
              <meta charset="utf-8">
              <link rel="stylesheet" href="dist/base.css" type="text/css" />
          </head>
          <body class="m-0">
              <div class="py-4">
                  <div class="container">
                      <h2>Welcome to <strong>Galaxy v{{ .Chart.AppVersion }}</strong></h2>
                      <br>
                      <a target="_blank" href="https://docs.galaxyproject.org/en/master/" class="btn btn-primary">Documentation »</a>
                      <a target="_blank" href="https://galaxyproject.org" class="btn btn-primary">Community Hub »</a>
                  </div>
                  <br>
                  {{- if .Values.influxdb.enabled }}
                  <div class="container">
                      <iframe width="100%" height="1300px" frameborder="0" marginheight="0" marginwidth="0"
                          src="/grafana/d/gxy_general_stats_{{ .Release.Name }}/galaxy-overview?refresh=60s&orgId=1&kiosk&theme=light"></iframe>
                  </div>
                  {{- end }}
              </div>
              <div class="container">
                  <footer class="text-center">
                      <p>Galaxy v{{ .Chart.AppVersion }}, Helm Chart v{{ .Chart.Version }}</p>
                  </footer>
              </div>
          </body>
      </html>

influxdb:
  enabled: false
  url: ""
  username: ""
  password: ""

nginx:
  galaxyStaticDir: "/galaxy/server/static"
  image:
    repository: nginx
    tag: 1.22.0
    pullPolicy: IfNotPresent
  containerPort: 7080
  conf:
    client_max_body_size: 100g
  resources:
    # We recommend updating these based on the usage levels of the server
    requests:
      cpu: 100m
      memory: 500M
      ephemeral-storage: 10Gi
    limits:
      cpu: 2
      memory: 3G
      ephemeral-storage: 100Gi

tusd:
  enabled: true
  replicaCount: 1
  annotations: {}
  podAnnotations: {}
  podSpecExtra: {}
  securityContext:
    runAsUser: 101
    runAsGroup: 101
    fsGroup: 101
  image:
    repository: tusproject/tusd
    tag: v1.13.0
    pullPolicy: IfNotPresent
  ingress:
    enabled: true
    ingressClassName: nginx
    annotations:
      nginx.ingress.kubernetes.io/proxy-request-buffering: "off"
      nginx.ingress.kubernetes.io/proxy-buffering: "off"
      nginx.ingress.kubernetes.io/proxy-http-version: "1.1"
      nginx.ingress.kubernetes.io/connection-proxy-header: "Upgrade"
      nginx.ingress.kubernetes.io/proxy-body-size: "0"
    hosts:
      - host: ~
        paths:
          - path: "/galaxy/api/upload/resumable_upload"
    tls: []

rabbitmq:
  enabled: true
  deploy: true
  existingCluster:
  existingSecret: '{{ include "galaxy-rabbitmq.fullname" . }}-default-user'
  protocol: amqp
  port: 5672
  nameOverride: rabbitmq
  extraSpec: {}
  terminationGracePeriodSeconds: 90
  persistence:
    storageClassName:
    storage: