Skip to content

Fix --shed_install for gxformat2 workflows#1182

Merged
jmchilton merged 4 commits intogalaxyproject:masterfrom
mvdbeek:fix_shed_install_for_gxformat2_workflows
Jul 22, 2021
Merged

Fix --shed_install for gxformat2 workflows#1182
jmchilton merged 4 commits intogalaxyproject:masterfrom
mvdbeek:fix_shed_install_for_gxformat2_workflows

Conversation

@mvdbeek
Copy link
Member

@mvdbeek mvdbeek commented Jul 21, 2021

No description provided.

@nsoranzo
Copy link
Member

Do we need to add a test for this? I couldn't find a Format 2 workflow with tool_shed_repository in tests/ .

with open(path, "r") as f:
workflow = yaml.safe_load(f)

tools = workflow.get("tools", [])
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I liked the idea of the workflows also serving as ephemeris installable entities - so the workflow could just have a list of repos to install. I guess that never made it into the schema though 🤔.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

We should make the tool ids resolvable, then we don't need this duplication (or the tool_shed_repositories entry in general) and we could finally get away from the repository concept 🙏.

@mvdbeek mvdbeek force-pushed the fix_shed_install_for_gxformat2_workflows branch from 54cdd39 to 23f1abf Compare July 21, 2021 15:58
@mvdbeek mvdbeek force-pushed the fix_shed_install_for_gxformat2_workflows branch from 23f1abf to cae73b4 Compare July 21, 2021 16:09
@jmchilton jmchilton merged commit 740178a into galaxyproject:master Jul 22, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants