mkdocs.yml

site_name: Docs CSC
site_url: https://docs.csc.fi/
site_description: Instructions and user guides for the CSC supercomputers, cloud services, storage and software, including FAQ and tutorials

repo_name: CSCfi/csc-user-guide
repo_url: https://github.com/CSCfi/csc-user-guide/
edit_uri: edit/master/docs/

extra:
  environment: !ENV [MKDOCS_ENV, "preview"]
  announcement_visible: true # Controls the visibility of the announcement bar
  landing_banner:
    path: https://a3s.fi/docs-files/banners/ # Put the image file in this bucket; Don't touch this value.
    image: example-banner.png
    title: Example banner now up on landing page
    link: https://example.org/courses/example-course/
    description: |-
      Banner for upcoming example course.
      Second line for example description.
    visible: false
  breadcrumbs_debug: !ENV DEBUG # Renders a debug view for breadcrumbs navigation
  analytics:
    provider: custom
    matomo_site_id: !ENV [MATOMO_SITE_ID, ""]
    matomo_url: !ENV [MATOMO_URL, ""]
    feedback:
      title: Do you find this page useful?
      ratings:
        - name: "Yes"
          type: Positive
          description: Yes! I do find this page useful.
          note: >-
            Thank you for your feedback!
        - name: "No"
          type: Negative
          description: No! This page needs to be improved.
          note: >-
            Thank you! Your feedback is appreciated.
      exclude:
        - ref.md
  short_description: User guides and tutorials
  social:
    - icon: material/github
      link: https://github.com/CSCfi/
    - icon: material/linkedin
      link: https://www.linkedin.com/company/csc---it-center-for-science/
    - icon: material/instagram
      link: https://www.instagram.com/CSCfi/
    - icon: material/facebook
      link: https://www.facebook.com/CSCfi/
    - icon: material/youtube
      link: https://www.youtube.com/c/CSCfi


hooks:
  - hooks/archives.py
  - hooks/preview.py

plugins:
  - tags
  - search
  - git-revision-date-localized:
      enabled: !ENV [ENABLED_GIT_REVISION_DATE, true]
      fallback_to_build_date: true
      type: date
      custom_format: "%Y-%m-%dT%H:%M:%S%z" # Used with feedback buttons
      locale: en
      timezone: Europe/Helsinki
      exclude:
        - index.md
        - support/archives/*.md
        - support/glossary.md
        - support/whats-new.md
        - apps/index.md
        - apps/by_discipline.md
        - apps/by_system.md
        - apps/by_license.md
  - section-index
  - redirects:
      redirect_maps:
        # deprecation:
        "support/tutorials/nomachine-usage.md": "apps/nomachine.md"
        "support/faq/cannot-login-from-nomachine.md": "apps/nomachine.md"
        "support/tutorials/puhti_quick.md": "support/tutorials/hpc-quick.md"
        "support/tutorials/mahti_quick.md": "support/tutorials/hpc-quick.md"
        # renamed files:
        "cloud/csc_notebooks/what_is_new.md": "support/whats-new.md#cloud-services"
        "cloud/csc_notebooks/concepts.md": "cloud/noppe/concepts.md"
        "cloud/csc_notebooks/data_persistence.md": "cloud/noppe/data_persistence.md"
        "cloud/csc_notebooks/guide_for_students.md": "cloud/noppe/guide_for_students.md"
        "cloud/csc_notebooks/guide_for_teachers.md": "cloud/noppe/guide_for_teachers.md"
        "cloud/csc_notebooks/index.md": "cloud/noppe/index.md"
        "computing/overview.md": "computing/index.md"
        "cloud/concepts.md": "cloud/index.md"
        "apps/alpha.md": "apps/index.md"
        "support/tutorials/env-guide/overview.md": "support/tutorials/env-guide/index.md"
        "computing/cProfile.md": "apps/cProfile.md"
        "computing/compute-san.md": "apps/compute-san.md"
        "computing/cuda-gdb.md": "apps/cuda-gdb.md"
        "computing/gdb.md": "apps/gdb.md"
        "computing/ncu.md": "apps/ncu.md"
        "computing/nsys.md": "apps/nsys.md"
        "computing/nvprof.md": "apps/nvprof.md"
        "computing/pdb.md": "apps/pdb.md"  
        # files moved to Allas:
        # (note the '<filename>.<original extension>.md' hack, as these are not Markdown files)
        "data/sensitive-data/federated-ega-pricing.pdf.md": "https://a3s.fi/docs-files/sensitive-data/PDF_instructions/federated-ega-pricing.pdf"
        # for URL consistency:
        "sensitive-data.md": "data/sensitive-data/index.md"
        "applications.md": "apps/index.md"
        "faq.md": "support/faq/index.md"
        "tutorials.md": "support/tutorials/index.md"
        "training-material.md": "support/training-material/index.md"
        "contact.md": "support/contact.md"
        "whats-new.md": "support/whats-new.md"
        # for convenience:
        "glossary.md": "support/glossary.md"
        "archives.md": "support/contact.md#archives"
        "mahti-nvme-2025.md": "support/wn/comp-new.md#new-small-partition-with-high-performance-nvme-storage-on-mahti-1322025"
        # Rahti2 to Rahti:
        "cloud/rahti2/catalog-docs.md": "cloud/rahti/catalog-docs.md"
        "cloud/rahti2/rahti-migration.md": "cloud/rahti/rahti-migration.md"
        "cloud/rahti2/index.md": "cloud/rahti/index.md"
        "cloud/rahti2/advanced.md": "cloud/rahti/advanced.md"
        "cloud/rahti2/billing.md": "cloud/rahti/billing.md"
        "cloud/rahti2/rahti-what-is.md": "cloud/rahti/rahti-what-is.md"
        "cloud/rahti2/concepts.md": "cloud/rahti/concepts.md"
        "cloud/rahti2/moving-into.md": "cloud/rahti/moving-into.md"
        "cloud/rahti2/ext_docs.md": "cloud/rahti/ext_docs.md"
        "cloud/rahti2/access.md": "cloud/rahti/access.md"
        "cloud/rahti2/networking.md": "cloud/rahti/networking.md"
        "cloud/rahti2/storage/index.md": "cloud/rahti/storage/index.md"
        "cloud/rahti2/storage/persistent.md": "cloud/rahti/storage/persistent.md"
        "cloud/rahti2/storage/expand-volumes.md": "cloud/rahti/storage/expand-volumes.md"
        "cloud/rahti2/storage/volume-snapshot.md": "cloud/rahti/storage/volume-snapshot.md"
        "cloud/rahti2/storage/ephemeral.md": "cloud/rahti/storage/ephemeral.md"
        "cloud/rahti2/storage/objectstorage.md": "cloud/rahti/storage/objectstorage.md"
        "cloud/rahti2/containers.md": "cloud/rahti/containers.md"
        "cloud/rahti2/security-guide.md": "cloud/rahti/security-guide.md"
        "cloud/rahti2/tutorials/index.md": "cloud/rahti/tutorials/index.md"
        "cloud/rahti2/tutorials/allow-pull-from-other-projects.md": "cloud/rahti/tutorials/allow-pull-from-other-projects.md"
        "cloud/rahti2/tutorials/deploy_static_webserver_webconsole.md": "cloud/rahti/tutorials/deploy_static_webserver_webconsole.md"
        "cloud/rahti2/tutorials/webhooks.md": "cloud/rahti/tutorials/webhooks.md"
        "cloud/rahti2/tutorials/annotations.md": "cloud/rahti/tutorials/annotations.md"
        "cloud/rahti2/tutorials/connect-database-hpc.md": "cloud/rahti/tutorials/connect-database-hpc.md"
        "cloud/rahti2/tutorials/yaml_introduction.md": "cloud/rahti/tutorials/yaml_introduction.md"
        "cloud/rahti2/tutorials/web-app-dev-cloud.md": "cloud/rahti/tutorials/web-app-dev-cloud.md"
        "cloud/rahti2/tutorials/sidecar_proxy_authentication.md": "cloud/rahti/tutorials/sidecar_proxy_authentication.md"
        "cloud/rahti2/tutorials/deploy_static_webserver_cli.md": "cloud/rahti/tutorials/deploy_static_webserver_cli.md"
        "cloud/rahti2/tutorials/custom-domain.md": "cloud/rahti/tutorials/custom-domain.md"
        "cloud/rahti2/tutorials/email.md": "cloud/rahti/tutorials/email.md"
        "cloud/rahti2/tutorials/http-redirector.md": "cloud/rahti/tutorials/http-redirector.md"
        "cloud/rahti2/tutorials/multi-stage-builds.md": "cloud/rahti/tutorials/multi-stage-builds.md"
        "cloud/rahti2/tutorials/ci_cd_introduction.md": "cloud/rahti/tutorials/ci_cd_introduction.md"
        "cloud/rahti2/tutorials/advanced-NetworkPolicies-networking.md": "cloud/rahti/tutorials/advanced-NetworkPolicies-networking.md"
        "cloud/rahti2/tutorials/pod-affinity.md": "cloud/rahti/tutorials/pod-affinity.md"
        "cloud/rahti2/tutorials/kustomize.md": "cloud/rahti/tutorials/kustomize.md"
        "cloud/rahti2/tutorials/4cat.md": "cloud/rahti/tutorials/4cat.md"
        "cloud/rahti2/usage/cli.md": "cloud/rahti/usage/cli.md"
        "cloud/rahti2/usage/projects_and_quota.md": "cloud/rahti/usage/projects_and_quota.md"
        "cloud/rahti2/usage/getting_started.md": "cloud/rahti/usage/getting_started.md"
        "cloud/rahti2/images/creating.md": "cloud/rahti/images/creating.md"
        "cloud/rahti2/images/keeping_docker_images_small.md": "cloud/rahti/images/keeping_docker_images_small.md"
        "cloud/rahti2/images/overview.md": "cloud/rahti/images/overview.md"
        "cloud/rahti2/images/Using_Rahti_2_integrated_registry.md": "cloud/rahti/images/Using_Rahti_integrated_registry.md"

markdown_extensions:
  - md_in_html
  - footnotes
  - admonition
  - abbr
  - attr_list
  - def_list
  - pymdownx.details
  - pymdownx.blocks.caption
  - pymdownx.tabbed:
      alternate_style: true
      slugify: !!python/object/apply:pymdownx.slugs.slugify
        kwds:
          case: lower
  - pymdownx.snippets:
      base_path: csc-overrides/assets/snippets
      auto_append:
        - glossaries/hpc.md
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.highlight:
      anchor_linenums: true
      line_spans: __span
      pygments_lang_class: true
  - pymdownx.inlinehilite
  - pymdownx.emoji:
      emoji_index: !!python/name:material.extensions.emoji.twemoji
      emoji_generator: !!python/name:material.extensions.emoji.to_svg

theme:
  name: material
  language: en
  custom_dir: csc-overrides
  logo: assets/images/logo.svg
  favicon: assets/images/logo.png
  icon:
    repo: material/git
    edit: material/pencil
    admonition:
      info: material/information
      success: material/check-circle
      warning: material/alert
    # Error admonition type is not in Material for MkDocs,
    # so the following icon is a literal definition in
    # csc-overrides/assets/stylesheets/admonition.css
      # error: material/close-circle
  palette:
    scheme: csc
    primary: custom
    accent: custom
  font: false # No loading fonts from G****e
  features:
    - content.action.edit
    - content.code.copy

extra_css:
  - assets/stylesheets/extra.css

extra_javascript:
  - assets/javascripts/extra.js
  - assets/javascripts/feedback.js

# See https://www.mkdocs.org/user-guide/configuration/#validation
validation:
  nav:
    omitted_files: ignore
  links:
    absolute_links: relative_to_docs
    unrecognized_links: warn
    anchors: warn

nav:
  - Home: index.md
  - Accounts:
      - accounts/index.md
      - Creating a new user account: accounts/how-to-create-new-user-account.md
      - User account lifecycle: accounts/account-lifecycle.md
      - Changing your password: accounts/how-to-change-password.md
      - Managing user information: accounts/how-to-manage-user-information.md
      - Creating a new project: accounts/how-to-create-new-project.md
      - When your project handles personal data: accounts/when-your-project-handles-personal-data.md
      - Adding members to your project: accounts/how-to-add-members-to-project.md
      - Adding service access for your project: accounts/how-to-add-service-access-for-project.md
      - Managing your project: accounts/how-to-manage-your-project.md
      - Applying for billing units: accounts/how-to-apply-for-billing-units.md
      - Increasing disk quotas: accounts/how-to-increase-disk-quotas.md
      - Accessing Mahti large partition: accounts/how-to-access-mahti-large-partition.md
      - Reviewing billing unit usage: accounts/how-to-view-billing-unit-usage.md
      - Billing: accounts/billing.md
      - Multi-factor authentication: accounts/mfa.md
      - Strong identification: accounts/strong-identification.md
      - FMI: accounts/fmi.md
  - Computing:
      - computing/index.md
      - Usage policy: computing/usage-policy.md
      - Billing: computing/hpc-billing.md
      - Systems:
          - computing/available-systems.md
          - Puhti: computing/systems-puhti.md
          - Mahti: computing/systems-mahti.md
          - Roihu: computing/systems-roihu.md
          - LUMI: "https://docs.lumi-supercomputer.eu/hardware/"
      - Connecting:
          - computing/connecting/index.md
          - Setting up SSH keys: computing/connecting/ssh-keys.md
          - SSH client on macOS and Linux: computing/connecting/ssh-unix.md
          - SSH client on Windows: computing/connecting/ssh-windows.md
      - Supercomputer storage:
          - computing/disk.md
          - Lustre filesystem: computing/lustre.md
          - Allas object storage: computing/allas.md
      - Module environment: computing/modules.md
      - Running jobs:
          - computing/running/getting-started.md
          - Create Puhti batch jobs: computing/running/creating-job-scripts-puhti.md
          - Puhti example scripts: computing/running/example-job-scripts-puhti.md
          - Create Mahti batch jobs: computing/running/creating-job-scripts-mahti.md
          - Mahti example scripts: computing/running/example-job-scripts-mahti.md
          - Submitting a job: computing/running/submitting-jobs.md
          - Available batch job partitions: computing/running/batch-job-partitions.md
          - High throughput: computing/running/throughput.md
          - Interactive usage: computing/running/interactive-usage.md
          - Performance checklist: computing/running/performance-checklist.md
      - Installing software:
          - computing/installing.md
          - Compiling on Puhti: computing/compiling-puhti.md
          - Compiling on Mahti: computing/compiling-mahti.md
          - Compiling on LUMI: computing/compiling-lumi.md
          - High performance libraries: computing/hpc-libraries.md
      - Debugging: computing/debugging.md
      - Performance analysis: computing/performance.md
      - Containers:
          - computing/containers/overview.md
          - Running containers: computing/containers/run-existing.md
          - Creating containers: computing/containers/creating.md
          - Container wrapper (Tykky): computing/containers/tykky.md
      - Web interface:
          - computing/webinterface/index.md
          - Connecting: computing/webinterface/connecting.md
          - Shell: computing/webinterface/shell.md
          - Files and storage services: computing/webinterface/file-browser.md
          - Project view: computing/webinterface/project-view.md
          - Interactive apps:
              - computing/webinterface/apps.md
              - Accelerated visualization: computing/webinterface/accelerated-visualization.md
              - Desktop: computing/webinterface/desktop.md
              - Jupyter: computing/webinterface/jupyter.md
              - Julia on Jupyter: computing/webinterface/julia-on-jupyter.md
              - Jupyter for courses: computing/webinterface/jupyter-for-courses.md
              - MATLAB: computing/webinterface/matlab.md
              - MLflow: computing/webinterface/mlflow.md
              - RStudio: computing/webinterface/rstudio.md
              - TensorBoard: computing/webinterface/tensorboard.md
              - Visual Studio Code: computing/webinterface/vscode.md
      - Quantum computing:
          - computing/quantum-computing/overview.md
          - Kvasi QLM:
              - Accessing Kvasi: computing/quantum-computing/kvasi/kvasi.md
              - Kvasi Billing: computing/quantum-computing/kvasi/kvasi-billing.md
          - Helmi:
              - Helmi projects: computing/quantum-computing/helmi/helmi-projects.md
              - Access Helmi through LUMI: computing/quantum-computing/helmi/helmi-from-lumi.md
              - First quantum job: computing/quantum-computing/helmi/first-quantum-job.md
              - Technical details: computing/quantum-computing/helmi/helmi-specs.md
              - FiQCI partition: computing/quantum-computing/helmi/fiqci-partition.md
              - Running on Helmi: computing/quantum-computing/helmi/running-on-helmi.md
  - Cloud Services:
      - cloud/index.md
      - Noppe:
          - cloud/noppe/index.md
          - Guide for students: cloud/noppe/guide_for_students.md
          - Guide for teachers: cloud/noppe/guide_for_teachers.md
          - Concepts: cloud/noppe/concepts.md
          - Data persistence: cloud/noppe/data_persistence.md
      - Pouta:
          - cloud/pouta/index.md
          # - What is Pouta: cloud/pouta/pouta-what-is.md
          # - Security Guidelines for Pouta: cloud/pouta/security.md
          # - Pouta Accounting Principles and Quotas: cloud/pouta/accounting.md
          # - Virtual machine flavors and Billing Unit rates: cloud/pouta/vm-flavors-and-billing.md
          - Getting started:
              - cloud/pouta/getting-started.md
              - Creating a virtual machine: cloud/pouta/launch-vm-from-web-gui.md
              - Connecting the virtual machine: cloud/pouta/connecting-to-vm.md
              - Command line:
                  - cloud/pouta/command-line-tools.md
                  - Install: cloud/pouta/install-client.md
          - Configuration:
              - cloud/pouta/configuration.md
              - VM lifecycle & saving BUs: cloud/pouta/vm-lifecycle.md
              - Virtual machine flavors and Billing Unit rates: cloud/pouta/vm-flavors-and-billing.md
              - Accounting principles and quotas: cloud/pouta/accounting.md
              - Images:
                  - cloud/pouta/images.md
                  - Creating, Converting, Uploading and Sharing virtual machine images: cloud/pouta/adding-images.md
              - Networking:
                  - cloud/pouta/networking.md
              - Storage:
                  - cloud/pouta/storage.md
                  - Ephemeral storage: cloud/pouta/ephemeral-storage.md
                  - Persistent volumes: cloud/pouta/persistent-volumes.md
                  - Snapshots: cloud/pouta/snapshots.md
                  - Snapshot using QEMU: cloud/pouta/qemu-vm.md
                  - Multi-attach Cinder storage: cloud/pouta/multiattach.md
          - Advanced:
              - cloud/pouta/advanced.md
              - Additional services (email, dns): cloud/pouta/additional-services.md
              - API Access: cloud/pouta/api-access.md
              - Application credentials: cloud/pouta/application-credentials.md
              - Application Development Practises: cloud/pouta/application-dev.md
              - Known problems and limitations: cloud/pouta/known-problems.md
              - Security Guidelines for Pouta: cloud/pouta/security.md
              # - Self study and troubleshooting:
              #     - Pouta videos: cloud/pouta/pouta-videos.md
          - Tutorials:
              - cloud/pouta/tutorials/index.md
              - cPouta and ePouta related videos: cloud/pouta/tutorials/pouta-videos.md
              - Learn cloud computing by developing and deploying a web application: cloud/pouta/tutorials/web-app-dev-cloud.md
              - Orchestration with Heat: cloud/pouta/tutorials/heat-orchestration.md
              - Create a jumphost in cPouta: cloud/pouta/tutorials/create-jumphost.md
              - SSH Key-pair: cloud/pouta/tutorials/ssh-key.md
              - Create a fixed IP for a VM: cloud/pouta/tutorials/create-fixed-ip-for-Vm.md
              - Set up a pipeline for pictures: cloud/pouta/tutorials/picture-pipeline.md
      - Pukki:
          - cloud/dbaas/index.md
          - What is DBaaS: cloud/dbaas/what-is-dbaas.md
          - Security Guides: cloud/dbaas/security-guides.md
          - Getting started with DBaaS:
              - cloud/dbaas/getting-started.md
              - Web interface: cloud/dbaas/web-interface.md
              - Command Line tools: cloud/dbaas/cli.md
              - Firewalls: cloud/dbaas/firewalls.md
              - Database Operations: cloud/dbaas/operations.md
              - Application Credentials: cloud/dbaas/application-credentials.md
          - Database sizes and prices: cloud/dbaas/flavors.md
          - Backups: cloud/dbaas/backups.md
          - Databases:
              - cloud/dbaas/databases.md
              - PostgreSQL:
                  - cloud/dbaas/postgresql.md
                  - Accessing your database: cloud/dbaas/postgres-accessing.md
                  - PostgreSQL version differences: cloud/dbaas/postgres-versions.md
                  - Extensions and parameters: cloud/dbaas/postgres-extensions.md
                  - Permissions: cloud/dbaas/postgres-permissions.md
              - MariaDB:
                  - cloud/dbaas/mariadb.md
                  - Accessing your database: cloud/dbaas/mariadb-accessing.md
                  - Permissions: cloud/dbaas/mariadb-permissions.md

          - More advanced features: cloud/dbaas/advanced.md
          - Resizing database instance volume: cloud/dbaas/resize-volume.md
      - Rahti:
          - cloud/rahti/index.md
          - What is Rahti:
              - cloud/rahti/rahti-what-is.md
              - Containers & their Orchestration: cloud/rahti/containers.md
              - Kubernetes and OpenShift concepts: cloud/rahti/concepts.md
              - External documentation: cloud/rahti/ext_docs.md
          - Getting Started:
              - Getting access: cloud/rahti/access.md
              - Web user interface: cloud/rahti/usage/getting_started.md
              - Command line tool: cloud/rahti/usage/cli.md
              - Moving into Rahti: cloud/rahti/moving-into.md
          - Configuration:
              - Billing: cloud/rahti/billing.md
              - Projects and quota: cloud/rahti/usage/projects_and_quota.md
              - Rahti Catalog: cloud/rahti/catalog-docs.md
              - Images:
                  - cloud/rahti/images/overview.md
                  - Creating an image: cloud/rahti/images/creating.md
                  - Keeping docker images small: cloud/rahti/images/keeping_docker_images_small.md
                  - Using Rahti integrated registry: cloud/rahti/images/Using_Rahti_integrated_registry.md
              - Storage in Rahti:
                  - cloud/rahti/storage/index.md
                  - Ephemeral storage: cloud/rahti/storage/ephemeral.md
                  - Persistent volumes: cloud/rahti/storage/persistent.md
                  - Object storage: cloud/rahti/storage/objectstorage.md
                  - Expand a volume: cloud/rahti/storage/expand-volumes.md
                  - Volume snapshot: cloud/rahti/storage/volume-snapshot.md
          - Advanced:
              - cloud/rahti/advanced.md
              - Networking: cloud/rahti/networking.md
              - Security guide: cloud/rahti/security-guide.md
          - Tutorials:
              - cloud/rahti/tutorials/index.md
              - 4cat: cloud/rahti/tutorials/4cat.md
              - Advanced NetworkPolicies: cloud/rahti/tutorials/advanced-NetworkPolicies-networking.md
              - Accessing databases on Rahti from CSC supercomputers: cloud/rahti/tutorials/connect-database-hpc.md
              - Allow pulls of images from one Rahti project to another: cloud/rahti/tutorials/allow-pull-from-other-projects.md
              - Annotations: cloud/rahti/tutorials/annotations.md
              - CI/CD on Rahti: cloud/rahti/tutorials/ci_cd_introduction.md
              - Custom domain names and secure transport: cloud/rahti/tutorials/custom-domain.md
              - Deploying a static web server using the command line: cloud/rahti/tutorials/deploy_static_webserver_cli.md
              - Deploying a static web server using the web interface: cloud/rahti/tutorials/deploy_static_webserver_webconsole.md
              - Kustomize: cloud/rahti/tutorials/kustomize.md
              - Learn cloud computing by developing and deploying a web application: cloud/rahti/tutorials/web-app-dev-cloud.md
              - Multi stage builds: cloud/rahti/tutorials/multi-stage-builds.md
              - Pod (anti) affinity: cloud/rahti/tutorials/pod-affinity.md
              - Reverse proxy authentication using a sidecar container: cloud/rahti/tutorials/sidecar_proxy_authentication.md
              - Sending e-mail from Rahti: cloud/rahti/tutorials/email.md
              - Setup a HTTP redirection in Rahti: cloud/rahti/tutorials/http-redirector.md
              - Short introduction to YAML: cloud/rahti/tutorials/yaml_introduction.md
              - Webhooks: cloud/rahti/tutorials/webhooks.md
              - OAuth2 Proxy: cloud/rahti/tutorials/oauth2.md
  - Data:
      - data/index.md
      #    - Datasets: data/datasets.md
      - Working with data:
          - data/datasets/dataset-sources.md
          - Tips for data management: data/datasets/datamanagement.md
          - Metadata and data documentation: data/datasets/metadata-and-documentation.md
          - Dataset sources: data/datasets/sourcing-datasets.md
          - Storing data at CSC: data/datasets/hosting-datasets-at-CSC.md
          - Publishing datasets: data/datasets/publishing-datasets.md
      - Moving data:
          - data/moving/index.md
          - Copying files using scp: data/moving/scp.md
          - Moving files using the HPC web interfaces: data/moving/web-interface.md
          - Graphical file transfer tools: data/moving/graphical_transfer.md
          - Using rsync for data transfer and synchronization: data/moving/rsync.md
          - Using tar and SSH to transfer many small files efficiently: data/moving/tar_ssh.md
          - Using wget to download data from web sites to CSC: data/moving/wget.md
          - Sharing and transporting files using Funet FileSender: data/moving/funet.md
          - Moving data between IDA and CSC computing environment: data/ida/using_ida.md
          - Remote disk mounts: data/moving/disk_mount.md
          - Copying data between Allas and IDA via Puhti: data/moving/copy_allas_ida.md
      - Allas object storage:
          - data/Allas/index.md
          - Introduction to Allas Storage service: data/Allas/introduction.md
          - Accessing Allas: data/Allas/accessing_allas.md
          - Common Use Cases: data/Allas/using_allas/common_use_cases.md
          - Common Error Messages: data/Allas/using_allas/error_messages.md
          - Allas object storage related terms and concepts: data/Allas/terms_and_concepts.md
          - Allas clients:
              - Allas Web UI: data/Allas/using_allas/allas-ui.md
              - a-command: data/Allas/using_allas/a_commands.md
              - a-backup: data/Allas/using_allas/a_backup.md
              - Cyberduck: data/Allas/using_allas/cyberduck.md
              - Python with S3: data/Allas/using_allas/python_boto3.md
              - Python with SWIFT: data/Allas/using_allas/python_swift.md
              - Rclone from Computing environment: data/Allas/using_allas/rclone.md
              - Rclone form Workstation: data/Allas/using_allas/rclone_local.md
              - Swift: data/Allas/using_allas/swift_client.md
              - S3cmd: data/Allas/using_allas/s3_client.md
              - Web GUI: data/Allas/using_allas/web_client.md
      # data/Allas/using_allas/directory_object_error.md is not linked in this structure
      - Kaivos database service:
          - data/kaivos/overview.md
          - Getting a database account: data/kaivos/kaivos-account.md
          - MySQL client programs at CSC: data/kaivos/kaivos_client_in_puhti.md
          - Data import and export: data/kaivos/kaivos_import.md
          - Using MySQL client through batch job system: data/kaivos/kaivos_batch_job.md
          - Using kaivos.csc.fi directly from your local computer: data/kaivos/kaivos_remote.md
          - Using Perl MySQL API at CSC: data/kaivos/kaivos_perl.md
          # Python MySQL API at CSC:
  - Sensitive data:
      - data/sensitive-data/index.md
      - Choose service: data/sensitive-data/choose-a-service.md
      - Store and analyse:
          - Start here:
              - data/sensitive-data/sd-access.md
              - Access as project manager: data/sensitive-data/sd-use-case-new-user-project-manager.md
              - Access as project member: data/sensitive-data/sd-use-case-new-user-project-member.md
          - Store with SD Connect:
              - data/sensitive-data/sd_connect.md
              - Login to SD Connect: data/sensitive-data/sd-connect-login.md
              - Upload: data/sensitive-data/sd-connect-upload.md
              - Share: data/sensitive-data/sd-connect-share.md
              - Download: data/sensitive-data/sd-connect-download.md
              - Delete: data/sensitive-data/sd-connect-delete.md
              - Command line interface: data/sensitive-data/sd-connect-command-line-interface.md
              - Troubleshooting: data/sensitive-data/sd-connect-troubleshooting.md
          - Analyse with SD Desktop:
              - data/sensitive-data/sd_desktop.md
              - Login to SD Desktop: data/sensitive-data/sd-desktop-login.md
              - Create virtual desktop: data/sensitive-data/sd-desktop-create.md
              - Manage virtual desktop: data/sensitive-data/sd-desktop-manage.md
              - Access virtual desktop: data/sensitive-data/sd-desktop-access-vm.md
              - Work with your virtual desktop: data/sensitive-data/sd-desktop-working.md
              - Customisation - software & tools: data/sensitive-data/sd-desktop-software.md
              - Import data: data/sensitive-data/sd-desktop-access.md
              - Export data via user interface: data/sensitive-data/sd-desktop-export.md
              - Export data programmatically: data/sensitive-data/sd-desktop-export-commandline.md
              - Troubleshooting: data/sensitive-data/sd-desktop-troubleshooting.md
      - Publish and reuse:
          - Publish with Federated EGA:
              - data/sensitive-data/federatedega.md
              - Publish data: data/sensitive-data/fega-submission.md
          - Reuse with SD Apply:
              - data/sensitive-data/sd-apply.md
              - Apply access to FEGA data: data/sensitive-data/sd-apply-access.md
              - Approve access to FEGA data: data/sensitive-data/sd-apply-approval.md
              - Enable reuse of FEGA data: data/sensitive-data/sd-apply-dac.md
      - Secondary use of health and social data:
          - Start here:
              - data/sensitive-data/secondarydata-access.md
              - Access with Findata permit: data/sensitive-data/findata-permit.md
              - Access with register permit: data/sensitive-data/single-register-permit.md
          - Analyse with SD Desktop for secondary use:
              - data/sensitive-data/sd-desktop-audited.md
              - Login to SD Desktop: data/sensitive-data/sd-desktop-secondary-login.md
              - Create virtual desktop: data/sensitive-data/sd-desktop-secondary-create.md
              - Manage virtual desktop: data/sensitive-data/sd-desktop-secondary-manage.md
              - Access virtual desktop: data/sensitive-data/sd-desktop-secondary-access-vm.md
              - Work with your desktop and software: data/sensitive-data/sd-desktop-secondary-working.md
              - Import data: data/sensitive-data/sd-desktop-secondary-access.md
              - Export data: data/sensitive-data/sd-desktop-secondary-export.md
              - Troubleshooting: data/sensitive-data/sd-desktop-secondary-troubleshooting.md
          - Instructions for registers: data/sensitive-data/single-register-submission.md
      - Terminology: data/sensitive-data/sd-terminology.md
  - Applications:
      - apps/index.md
      - By discipline: apps/by_discipline.md
      - By availability: apps/by_system.md
      - By license: apps/by_license.md
  - FAQ: support/faq/index.md
  - Tutorials: support/tutorials/index.md
  - Training material: support/training-material/index.md
  - Contact: support/contact.md
  - What's new: support/whats-new.md