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Update build and add testing process with ansible roles and packer vars#9

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eileen-xue wants to merge 4 commits intomainfrom
ansible-roles
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Update build and add testing process with ansible roles and packer vars#9
eileen-xue wants to merge 4 commits intomainfrom
ansible-roles

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@eileen-xue
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@eileen-xue eileen-xue commented Apr 1, 2026

  1. Update build process
    • Add packer vars (build/packer-vars) - openstack env vars
    • Add ansible roles (build/ansible/roles) - common, singularity, nextflow, rstudio, cvmfs, shelley-bio
    • Add ansible vars (build/ansible/vars) - CVMFS proxies, tools versions
    • Update to new Nirin flavor (c3ep.*)
    • Update OS & tool versions
      • Update Singularity, SHPC, Nextflow, Python, and Go versions
      • Update to Ubuntu 24.04, and some pkgs don't support Ubuntu version <= 22.04
    • Add build script (build/scripts)
  2. Add testing process
    • Add ansible test playbook (test-bioshell.yml)
    • Ansible test roles - validate_cvmfs, validate_nextflow, validate_jupyter, validate_rstudio, validate_shelley-bio
  3. Update README.md

@eileen-xue eileen-xue requested a review from Mitchob April 1, 2026 00:52
@Mitchob
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Mitchob commented Apr 2, 2026

Testing PR #9 (Update build and add testing process with ansible roles and packer vars) on Nectar.

Issues encountered:

  1. The scripts build/scripts/nectar.sh and build/scripts/nirin.sh are not executable by default. You need to run:
chmod +x build/scripts/nectar.sh
chmod +x build/scripts/nirin.sh
  1. The build process fails at the Singularity installation tasks with this error:
fatal: [default]: FAILED! => {"changed": false, "msg": "No package matching 'libsubid-dev' is available"}

@eileen-xue
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Thanks for testing and providing the feedback.

  1. I will update and make scripts executable by default.
  2. On the first comment of this PR and updated README file, users will need to use Ubuntu 24.04 or above. Some packages are not available on old Ubuntu versions.

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