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 :doc:`Getting Started Guide `. 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 :doc:`End User Topics ` or our `quickstart guide `_. .. toctree:: :maxdepth: 1 Go to Dockstore systemstatus .. toctree:: :caption: About :maxdepth: 1 dockstore-introduction Dockstore Blog changelog faq news roadmap dictionary /assets/templates/template.rst Getting Started --------------- * :doc:`Intro to Dockstore Tools and Workflows ` * Getting started tutorial -- designed for people totally new to writing workflows and working with Docker 1. :doc:`Intro ` 2. :doc:`Docker ` 3. Language-specific introductions * :doc:`Common Workflow Language (CWL) ` * :doc:`Workflow Description Language (WDL) ` * :doc:`Nextflow (NFL) ` * :doc:`Galaxy ` 4. :doc:`Creating a Dockstore Account ` 5. :doc:`Register a tool on Dockstore ` 6. :doc:`Register a workflow on Dockstore ` 7. :doc:`Archive an Entry on Dockstore ` 8. :doc:`Delete an Entry on Dockstore ` 9. :doc:`Hosted tools and workflows ` * :doc:`Notebooks ` * :doc:`Services (preview) ` * :doc:`Registering tools, workflows, notebooks, and services with the Dockstore GitHub App ` .. toctree:: :caption: Getting Started (Tutorial) :maxdepth: 1 :hidden: 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 ^^^^^^^^^^^^^^ .. centered:: |AnVILLaunchWith|_ |CavaticaLaunchWith|_ |CGCLaunchWith|_ |DnanexusLaunchWith|_ |GalaxyLaunchWith|_ |SeqeraPlatformLaunchWith|_ |TerraLaunchWith|_ .. |AnVILLaunchWith| image:: /assets/images/square/anvil_text.png :alt: go to launch with AnVIL page :height: 140px .. _AnVILLaunchWith: launch-with/anvil-launch-with.html .. |CavaticaLaunchWith| image:: /assets/images/square/cavatica_text.png :alt: go to launch with Cavatica page :height: 140px .. _CavaticaLaunchWith: launch-with/cavatica-launch-with.html .. |CGCLaunchWith| image:: /assets/images/square/cgc_text.png :alt: go to launch with Cancer Genome Cloud (CGC) page :height: 140px .. _CGCLaunchWith: launch-with/cgc-launch-with.html .. |DnanexusLaunchWith| image:: /assets/images/square/dnanexus_text.png :alt: go to launch with DNA Nexus page :height: 140px .. _DnanexusLaunchWith: launch-with/dnanexus-launch-with.html .. |GalaxyLaunchWith| image:: /assets/images/square/galaxy_text.png :alt: go to launch with Galaxy page :height: 140px .. _GalaxyLaunchWith: launch-with/galaxy-launch-with.html .. |SeqeraPlatformLaunchWith| image:: /assets/images/square/seqeraplatform_text.png :alt: go to launch with Seqera Platform :height: 140px .. _SeqeraPlatformLaunchWith: launch-with/seqera-platform-launch-with.html .. |TerraLaunchWith| image:: /assets/images/square/terra_text.png :alt: go to launch with Terra page :height: 140px .. _TerraLaunchWith: launch-with/terra-launch-with.html In addition to the above cloud partners, you can also launch workflows with :doc:`BioData Catalyst ` or the :doc:`Dockstore CLI `. 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 ^^^^^^^^^^^^^^^^^^^^^ .. centered:: |GoogleColabLaunchWith|_ |GitHubCodespacesLaunchWith|_ |MyBinderLaunchWith|_ .. |GoogleColabLaunchWith| image:: /assets/images/square/google_colab_text.png :alt: go to launch with Google Colab page :height: 140px .. _GoogleColabLaunchWith: launch-with/google-colab-launch-with.html .. |GitHubCodespacesLaunchWith| image:: /assets/images/square/github_codespaces_text.png :alt: go to launch with GitHub Codespaces page :height: 140px .. _GitHubCodespacesLaunchWith: launch-with/github-codespaces-launch-with.html .. |MyBinderLaunchWith| image:: /assets/images/square/mybinder_text.png :alt: go to launch with MyBinder page :height: 140px .. _MyBinderLaunchWith: launch-with/mybinder-launch-with.html .. toctree:: :caption: Launch Tools and Workflows :maxdepth: 1 :hidden: 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/seqera-platform-launch-with launch-with/terra-launch-with .. toctree:: :caption: Launch Notebooks :maxdepth: 1 :hidden: launch-with/google-colab-launch-with launch-with/github-codespaces-launch-with launch-with/mybinder-launch-with .. toctree:: :caption: End user topics :maxdepth: 1 end-user-topics/end-user-topics end-user-topics/faceted-search end-user-topics/starring end-user-topics/language-support end-user-topics/ORCID end-user-topics/dois .. toctree:: :caption: Videos (tutorials & presentations) :maxdepth: 1 videos Best practices guidelines ------------------------- * Language-specific: :doc:`CWL ` | :doc:`Nextflow ` | :doc:`WDL ` * :doc:`Best practices on Dockstore ` * :doc:`Best practices for secure and FAIR workflows ` * :doc:`Notebook portability ` .. toctree:: :caption: Best Practices :maxdepth: 1 :hidden: 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 .. toctree:: :caption: Dockstore CLI :maxdepth: 1 Installing the Dockstore CLI 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 ------------------------- .. include:: advanced-topics/advanced-topics.rst .. To get the above to format nicely, I made changes to advanced-topics/advanced-topics that make it no longer compatible with the Table of Contents, so advanced-topics/advanced-topics will no longer show in the sidebar. I feel that is a fair trade off. * :doc:`Dockstore Tools Overhaul ` * :doc:`Detailed comparison of tools and workflows ` * :doc:`Legacy features ` * :doc:`Docker registries ` * :doc:`Public and private tools ` * :doc:`Checker workflows `, and :doc:`how to run them using TRS ` * :doc:`Sharing workflows ` * :doc:`Aliases ` * :doc:`Docker alternatives ` * Maximizing reproducibility * :doc:`Creating snapshots and requesting DOIs ` * :doc:`Checksum for files and Docker Images ` * :doc:`Verified workflows and tools ` * :doc:`Workflow metrics ` * :doc:`Organizations and collections ` .. Purposely not including "posting zips" as it is depreciated, but it is still in the sidebar .. toctree:: :caption: Advanced Developer Topics :maxdepth: 1 :hidden: 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/posting-zips advanced-topics/verification advanced-topics/metrics advanced-topics/organizations-and-collections advanced-topics/wes/cli-wes-tutorial .. toctree:: :caption: Extras :maxdepth: 1 BCC 2020 Docker Training BCC 2020 WDL Training posters-and-talks user-created Dockstore Logo Usage Guidelines .. centered:: In Affiliation with .. centered:: |CollabLink|_ |imagespace| |OicrLink|_ |imagespace| |Ga4ghLink|_ |imagespace| |UcscLink|_ .. |CollabLink| image:: /assets/images/affiliations/collaboratory.png :alt: collaboratory :height: 55px .. _CollabLink: https://doi.org/10.1158/1538-7445.AM2017-378 .. |OicrLink| image:: /assets/images/affiliations/oicr.png :alt: oicr :height: 55px .. _OicrLink: https://oicr.on.ca/ .. |Ga4ghLink| image:: /assets/images/affiliations/ga4gh.png :alt: ga4gh :height: 55px .. _Ga4ghLink: https://www.ga4gh.org .. |UcscLink| image:: /assets/images/affiliations/ucsc.png :alt: ucsc :height: 55px .. _UcscLink: https://genomics.ucsc.edu/ .. centered:: Workflow Languages .. centered:: |CwlLink|_ |imagespace| |WdlLink|_ |imagespace| |NflLink|_ |imagespace| |GalaxyLink|_ .. |CwlLink| image:: /assets/images/affiliations/cwl.png :alt: cwl :height: 65px .. _CwlLink: https://www.commonwl.org/ .. |WdlLink| image:: /assets/images/affiliations/wdl.png :alt: wdl :height: 45px .. _WdlLink: https://openwdl.org/ .. |NflLink| image:: /assets/images/affiliations/nfl.png :alt: nextflow :height: 45px .. _NflLink: https://www.nextflow.io/ .. |GalaxyLink| image:: /assets/images/affiliations/galaxy.png :alt: galaxy :height: 55 px .. _GalaxyLink: https://galaxyproject.org/ .. centered:: Works With .. centered:: |SevenBridgesLink|_ |imagespace| |TerraLink|_ .. |SevenBridgesLink| image:: /assets/images/affiliations/sevenbridges.png :alt: sevenbridges :height: 45px .. _SevenBridgesLink: https://www.sevenbridges.com/ .. |TerraLink| image:: /assets/images/affiliations/terra.png :alt: terra :height: 75px .. _TerraLink: https://terra.bio/ .. |imagespace| unicode:: U+00A0 U+00A0 U+00A0 U+00A0 U+00A0 .. non-breaking spaces between logo images .. centered:: |horizontalline| .. |horizontalline| image:: /assets/images/hori_line.png :alt: line :height: 25 px