Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Detects OOM for CellBrowser even if tool exits with 0 code. #296

Merged
merged 3 commits into from
Jul 15, 2023

Conversation

pcm32
Copy link
Member

@pcm32 pcm32 commented Jul 5, 2023

Description

cbScanpyImport, part of UCSC CellBrowser, exists with code 0 (no error) on Out of memory kill signal. This handles the process more gracefully so that Galaxy can understand it actually failed and needs to be resubmitted.

Handles maximilianh/cellBrowser#263 (at least in the Kubernetes case)

Type of change

  • Bug fix (non-breaking change which fixes an issue)
  • New feature (non-breaking change which adds functionality)
  • Breaking change (fix or feature that would cause existing functionality to not work as expected)
  • This change requires a documentation update

Checklist

  • I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
  • If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
  • If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1). It is acceptable to do this as well when the cli version changed but not the underlying tool (to avoid issues in the coming point).
  • If I changed the version, the @TOOL_VERSION@ part of the version does not contain any + symbols within, otherwise this will break tool ordering on the interface and the default tool being picked. Tool version should always conform to PEP440 to avoid this issue. The only + should be the one preceding galaxy<build> (unless that all the versions from that tool previously followed a different pattern).

@pcm32 pcm32 merged commit 30c2320 into develop Jul 15, 2023
4 checks passed
@pcm32 pcm32 deleted the feature/fix_cell_browser_oom branch July 15, 2023 09:12
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.

1 participant