index.rst

Welcome to Dockstore Documentation!

Note

Our code lives on GitHub at dockstore/dockstore and dockstore/dockstore-ui2.

Dockstore is an open platform used by the GA4GH for sharing reproducible and interoperable tools, workflows, and services. For tools and workflows, we support Common Workflow Language (CWL), Workflow Description Language (WDL), Nextflow (NFL), and Galaxy.

If this is your first time learning about Dockstore, we recommend starting with the Getting Started Guide <getting-started/getting-started>. This will introduce you to the core concepts of Dockstore, leaving you with a good understanding of the platform. However, if you are simply looking to launch tools and workflows, we recommend going straight to the End User Topics <end-user-topics/end-user-topics> or our quickstart guide.

Go to Dockstore <https://dockstore.org> systemstatus

dockstore-introduction Dockstore Blog <https://medium.com/dockstore> changelog faq news roadmap dictionary /assets/templates/template.rst

Getting Started

• Intro to Dockstore Tools and Workflows </getting-started/intro-to-dockstore-tools-and-workflows>

• Getting started tutorial -- designed for people totally new to writing workflows and working with Docker

  1. Intro </getting-started/getting-started>
  2. Docker <getting-started/getting-started-with-docker>

  3. Language-specific introductions

     • Common Workflow Language (CWL) <getting-started/getting-started-with-cwl>
     • Workflow Description Language (WDL) <getting-started/getting-started-with-wdl>
     • Nextflow (NFL) <getting-started/getting-started-with-nextflow>
     • Galaxy <getting-started/getting-started-with-galaxy>

  4. Creating a Dockstore Account <getting-started/register-on-dockstore>
  5. Register a tool on Dockstore <getting-started/dockstore-tools>
  6. Register a workflow on Dockstore <getting-started/dockstore-workflows>
  7. Archive an Entry on Dockstore <getting-started/archive-on-dockstore>
  8. Delete an Entry on Dockstore <getting-started/delete-on-dockstore>
  9. Hosted tools and workflows <getting-started/hosted-tools-and-workflows>

• Notebooks <getting-started/getting-started-with-notebooks>
• Services (preview) <getting-started/getting-started-with-services>
• Registering tools, workflows, notebooks, and services with the Dockstore GitHub App <getting-started/github-apps/github-apps-landing-page>

getting-started/getting-started getting-started/intro-to-dockstore-tools-and-workflows getting-started/getting-started-with-docker getting-started/getting-started-with-cwl getting-started/getting-started-with-wdl getting-started/getting-started-with-nextflow getting-started/getting-started-with-galaxy getting-started/register-on-dockstore getting-started/dockstore-tools getting-started/dockstore-workflows getting-started/archive-on-dockstore getting-started/delete-on-dockstore getting-started/hosted-tools-and-workflows getting-started/getting-started-with-services getting-started/getting-started-with-notebooks getting-started/github-apps/github-apps-landing-page

Launching tools and workflows from Dockstore

Dockstore partners with several compute platforms, allowing you to export workflows into these platforms with the click of a button. We also provide a CLI to run tools and workflows locally. Click on the links below for more information.

Cloud Partners

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In addition to the above cloud partners, you can also launch workflows with BioData Catalyst <launch-with/bdcat-launch-with> or the Dockstore CLI <launch-with/launch>.

Launching notebooks from Dockstore

Dockstore supports launching notebooks into several environments with the click of a button. Click on the links below for more information.

Notebook Environments

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launch-with/launch launch-with/anvil-launch-with launch-with/bdcat-launch-with launch-with/cavatica-launch-with launch-with/cgc-launch-with launch-with/dnanexus-launch-with launch-with/galaxy-launch-with launch-with/nextflow-tower-launch-with launch-with/terra-launch-with

launch-with/google-colab-launch-with launch-with/github-codespaces-launch-with launch-with/mybinder-launch-with

end-user-topics/end-user-topics end-user-topics/faceted-search end-user-topics/starring end-user-topics/language-support end-user-topics/ORCID

videos

Best practices guidelines

• Language-specific: CWL <advanced-topics/best-practices/cwl-best-practices> | Nextflow <advanced-topics/best-practices/nfl-best-practices> | WDL <advanced-topics/best-practices/wdl-best-practices>
• Best practices on Dockstore <advanced-topics/best-practices/best-practices-dockstore>
• Best practices for secure and FAIR workflows <advanced-topics/best-practices/best-practices-secure-fair-workflows>
• Notebook portability <advanced-topics/best-practices/notebook-portability>

advanced-topics/best-practices/cwl-best-practices advanced-topics/best-practices/wdl-best-practices advanced-topics/best-practices/nfl-best-practices advanced-topics/best-practices/best-practices-dockstore advanced-topics/best-practices/best-practices-secure-fair-workflows advanced-topics/best-practices/best-practices-development advanced-topics/best-practices/notebook-portability

Installing the Dockstore CLI <https://dockstore.org/quick-start> advanced-topics/dockstore-cli/overview advanced-topics/dockstore-cli/dockstore-cli-faq advanced-topics/dockstore-cli/local-cromwell-config advanced-topics/dockstore-cli/set-up-file-provisioning-plugins advanced-topics/dockstore-cli/developing-file-provisioning-plugins advanced-topics/dockstore-cli/advanced-features advanced-topics/dockstore-cli/yaml-command-line-validator-tool

Advanced developer topics

• Dockstore Tools Overhaul <advanced-topics/dockstore-tools-overhaul>
• Detailed comparison of tools and workflows <advanced-topics/tools-vs-workflows>
• Legacy features <advanced-topics/legacy/legacy>
• Docker registries <advanced-topics/docker-registries>
• Public and private tools <advanced-topics/public-and-private-tools>
• Checker workflows <advanced-topics/checker-workflows>, and how to run them using TRS <advanced-topics/checker-workflow-trs>
• Sharing workflows <advanced-topics/sharing-workflows>
• Aliases <advanced-topics/guid-alias>
• Docker alternatives <advanced-topics/docker-alternatives>

• Maximizing reproducibility

  • Creating snapshots and requesting DOIs <advanced-topics/snapshot-and-doi>
  • Checksum for files and Docker Images <advanced-topics/checksum-support>

• GA4GH Write API (intended as a proof-of-concept and for developers with a large number of tools) <advanced-topics/conversions>
• Using batch services (AWS, Azure, Google, and Consonance) <advanced-topics/batch-services>
• Verified workflows and tools <advanced-topics/verification>
• Workflow metrics <advanced-topics/metrics>
• Organizations and collections <advanced-topics/organizations-and-collections>

advanced-topics/dockstore-tools-overhaul advanced-topics/tools-vs-workflows advanced-topics/legacy/legacy advanced-topics/docker-registries advanced-topics/public-and-private-tools advanced-topics/checker-workflows advanced-topics/checker-workflow-trs advanced-topics/sharing-workflows advanced-topics/guid-alias advanced-topics/docker-alternatives advanced-topics/snapshot-and-doi advanced-topics/checksum-support advanced-topics/conversions advanced-topics/batch-services advanced-topics/aws-batch advanced-topics/azure-batch advanced-topics/posting-zips advanced-topics/verification advanced-topics/metrics advanced-topics/organizations-and-collections advanced-topics/wes/cli-wes-tutorial

BCC 2020 Docker Training </docker_instructions> BCC 2020 WDL Training </wdl_instructions> posters-and-talks user-created Dockstore Logo Usage Guidelines </dockstore-logo-usage-guidelines>

In Affiliation with

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Workflow Languages

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Works With

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