Skip to content

{bio}[system/system] sentieon-genomics v202503.02#25119

Merged
smoors merged 8 commits intoeasybuilders:developfrom
nicorap:20260121175436_new_pr_sentieon-genomics20250302
Mar 9, 2026
Merged

{bio}[system/system] sentieon-genomics v202503.02#25119
smoors merged 8 commits intoeasybuilders:developfrom
nicorap:20260121175436_new_pr_sentieon-genomics20250302

Conversation

@nicorap
Copy link
Copy Markdown
Contributor

@nicorap nicorap commented Jan 21, 2026

(created using eb --new-pr)

@github-actions github-actions Bot added manual_download Sources require manual download new labels Jan 21, 2026
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
nicorap and others added 5 commits March 9, 2026 08:33
…2503.02.eb


address non needed PATH.

Co-authored-by: Sam Moors <[email protected]>
…2503.02.eb


remove unnecessary end of line

Co-authored-by: Sam Moors <[email protected]>
…2503.02.eb


remove redundant check

Co-authored-by: Sam Moors <[email protected]>
Expanded the description to provide more details about the Sentieon Genomics toolkit and its requirements.
move jemalloc preload configuration in modluafooter under modextrapaths
@nicorap
Copy link
Copy Markdown
Contributor Author

nicorap commented Mar 9, 2026

Dear @smoors , thanks a lot for the comments. I have addressed all of them:

  • removed redundant PATH entry from modextrapaths
  • removed redundant bin sanity dir check
  • reordered sanity_check_paths, modextrapaths, and modluafooter
  • expanded the description a bit

Hope we can merge this one when you have time to look at it.

reformat file to pass ci/cd tests
@nicorap
Copy link
Copy Markdown
Contributor Author

nicorap commented Mar 9, 2026

and now ci/cd tests pass.

Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Comment thread easybuild/easyconfigs/s/sentieon-genomics/sentieon-genomics-202503.02.eb Outdated
Addresses comments: toolchain order,  removed modextrapaths,   added a handful of stable symlinked libs.
@nicorap
Copy link
Copy Markdown
Contributor Author

nicorap commented Mar 9, 2026

@smoors , thanks,I addressed the comments:

  • moved toolchain below description
  • removed modextrapaths, since LD_LIBRARY_PATH is added automatically
  • extended sanity_check_paths with a few bundled libraries from lib/
  • tested that tests pass.

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Mar 9, 2026

@nicorap can you submit a test report for this software? i don't have access to it, i cannot test it.

see here how to: https://docs.easybuild.io/integration-with-github/#github_upload_test_report

@nicorap
Copy link
Copy Markdown
Contributor Author

nicorap commented Mar 9, 2026

Test report by @nicorap
SUCCESS
Build succeeded for 1 out of 1 (total: 10 secs) (1 easyconfigs in total)
sw-build-01.hpc.cld - Linux Rocky Linux 9.7 (Blue Onyx), x86_64, AMD EPYC 9655 96-Core Processor (zen4), Python 3.9.25
See https://gist.github.com/nicorap/f6deb210415fbc2a6450e52232913ebc for a full test report.

@smoors smoors added this to the next release (5.2.2?) milestone Mar 9, 2026
Copy link
Copy Markdown
Contributor

@smoors smoors left a comment

Choose a reason for hiding this comment

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

lgtm

@smoors
Copy link
Copy Markdown
Contributor

smoors commented Mar 9, 2026

Going in, thanks @nicorap!

@smoors smoors merged commit 820287b into easybuilders:develop Mar 9, 2026
6 checks passed
@nicorap nicorap deleted the 20260121175436_new_pr_sentieon-genomics20250302 branch March 9, 2026 14:03
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

manual_download Sources require manual download new

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants