Add a mechanism or a protocol for noticing failures early.

To simplify acceptance testing on production instances it would be useful to have access to the Galaxy API to:

• upload workflows and install tools with Planemo
• upload datasets and histories
• run workflows
• query the instance for job statuses

Once the tests have been developed they can run at the Broad (i.e. on a local network and behind any firewalls). However, during development it would be necessary to access the Galaxy API from outside Terra.

Improve testing infrastructure to make tests run more reliably

Identify and debug problematic job runs.

Display a short history of results for each test.

Use the benchmarking results to calculate job costs.

Tasks:

• Install tools as your own admin
• Import/export data from workspace [export doesn’t work]
• Import/export history from workspace
• Import workflow (via url with /json or via .ga)
• Export workflow (save .ga or save .json)
• GTN: Run this tutorial on AnVIL
• GTN: Add galaxy-on-anvil tag to tutorials

See Also: GCC 2023 Cofest notes

update export workflow destination to myexperiment.org to WorkflowHub

How to save your configuration of Galaxy in AnVIL (image or startup script?) Possibility to write a Galaxy tool to export & import a Galaxy tool config as well as select histories (datasets?)

Could make it user friendly within a tool suite view - option to “define my own”, save the option, export it, and give you an option to do this on startup) [Galaxy]

Part of standard system maintenance and evolution. 23.1 release notes/status tracking issue.

• Make sure Galaxy image is building for 23.1; test locally
• Update Galaxy Helm to use 23.1; release new chart version
• Sync Galaxy AnVIL fork & build an image
• Update GKM
• Test on GKE
• Test on Terra BEE
• Update Leo & test in Dev
• Deploy to prod & announce

Import via URL with /json on the end [works]

ACTION: Natalie suggest to Marius to add a note in import workflow via url, it needs /json at the end.

Compare resource uasge prediction with benchmarks and costs.

make this the default tab, first option to import [social issue, UI/UX team].

May have considerations bc of 3rd party permissions

Already done in PR #323? Note caveats when the web hook is enabled.

Rendering if Dockstore markdown in Galaxy [follow up with Marius]

Exporting a dataset: directory_uri is getting sanitized which conflicts with Terra “Other Data” folder having a space in the name
ACTION: follow up with Luke on whether we can not auto sanitize, if we can only sanitize the highest level URI

Draft can be found here.

Import workflow via .ga in tutorial mode [works]

Implement tests

• Launch
• Stop
• Resume
• Delete

Update the list of tools being tested, ideally linking to use tool list on the CVMFS.

Unit testing

Benchmarks to perform

• RNA-Seq
• Variant calling
• Single cell
• High profile tools

In progress [Marius]