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Include rev in Toil appliance container#5549

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adamnovak merged 1 commit into
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issues/5548-arm-failure-fix-ci
Jul 1, 2026
Merged

Include rev in Toil appliance container#5549
adamnovak merged 1 commit into
masterfrom
issues/5548-arm-failure-fix-ci

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@adamnovak

@adamnovak adamnovak commented Jul 1, 2026

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Ubuntu 26.04 moved rev to bsdextrautils, which is not installed by default. But the CWL tests need it (see
common-workflow-language/cwl-v1.2#307), and users might want it too.

This will fix #5548.

Changelog Entry

To be copied to the draft changelog by merger:

  • Toil appliance container again includes the rev binary needed on the host to pass CWL conformance tests

Reviewer Checklist

  • Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
    • If it is coming from an external repo, make sure to pull it in for CI with:
      contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
      
    • If there is no associated issue, create one.
  • Read through the code changes. Make sure that it doesn't have:
    • Addition of trailing whitespace.
    • New variable or member names in camelCase that want to be in snake_case.
    • New functions without type hints.
    • New functions or classes without informative docstrings.
    • Changes to semantics not reflected in the relevant docstrings.
    • New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
    • New features without tests.
  • Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
  • Finish the review with an overall description of your opinion.

Merger Checklist

  • Make sure the PR passed tests, including the Gitlab tests, for the most recent commit in its branch.
  • Make sure the PR has been reviewed. If not, review it. If it has been reviewed and any requested changes seem to have been addressed, proceed.
  • Merge with the Github "Squash and merge" feature.
    • If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
  • Copy its recommended changelog entry to the Draft Changelog.
  • Append the issue number in parentheses to the changelog entry.

Ubuntu 26.04 moved `rev` to bsdextrautils, which is not installed by
default. But the CWL tests need it (see
common-workflow-language/cwl-v1.2#307), and
users might want it too.
@adamnovak
adamnovak merged commit 8593a3e into master Jul 1, 2026
3 checks passed
@adamnovak
adamnovak deleted the issues/5548-arm-failure-fix-ci branch July 1, 2026 23:23
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CWL ARM integration tests are failing

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