[TSPS-682] Update beagle docker image #1722

salonishah11 · 2025-11-17T14:44:11Z

Description

Jira: https://broadworkbench.atlassian.net/browse/TSPS-682

This PR updates the docker image for Phase and Impute tasks in ImputationBeagle wdl. The docker image contains Beagle jar that is generated from code that lives in GitHub repo tmp-sharing/imp-server. The reason for this is to have the code for Beagle jar in a version controlled place.

GHA run using Scientific type testing with this new docker image: https://github.com/broadinstitute/warp/actions/runs/19650001245

warp-tools PR: broadinstitute/warp-tools#176

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP team by tagging @broadinstitute/warp-admins in a comment on this PR.

Did you add inputs, outputs, or tasks to a workflow?
Did you modify, delete or move: file paths, file names, input names, output names, or task names?
If you made a changelog update, did you update the pipeline version number?

github-actions · 2025-11-17T14:44:21Z

Remember to squash merge!

github-actions · 2025-11-17T14:44:31Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
ImputationBeagle.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-17T14:44:32Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-19T20:05:30Z

Remember to squash merge!

github-actions · 2025-11-19T20:05:42Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-19T20:05:42Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
ImputationBeagle.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-20T15:01:39Z

Remember to squash merge!

github-actions · 2025-11-20T15:01:49Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-20T15:02:18Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
ImputationBeagle.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-21T19:39:36Z

Remember to squash merge!

github-actions · 2025-11-21T19:39:47Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
ImputationBeagle.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-21T19:39:49Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-21T20:50:25Z

Remember to squash merge!

github-actions · 2025-11-21T20:50:35Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-21T20:50:38Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
ImputationBeagle.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-24T20:04:06Z

Remember to squash merge!

github-actions · 2025-11-24T20:04:17Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
ImputationBeagle.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-24T20:04:26Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-25T14:27:03Z

Remember to squash merge!

github-actions · 2025-11-25T14:27:09Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2025-11-25T14:27:12Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-25T15:20:32Z

Remember to squash merge!

github-actions · 2025-11-25T15:20:43Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2025-11-25T15:20:45Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

salonishah11 · 2025-11-25T15:28:32Z

pipeline_versions.txt

 IlluminaGenotypingArray	 1.12.26	2025-10-09 
 Imputation	 1.1.23	2025-10-03 
-ImputationBeagle	 2.3.0	2025-11-12 
+ImputationBeagle	 2.4.0	2025-11-25 


I thought changing the Docker image and how Beagle jar is generated in docker image warrants for a minor version change but happy to discuss if this isn't right.

i think this is fine, patch would have been fine too since there is no "actual" changes to the output but your reasoning is very valid.

yeah I like the minor version change here

…tute/warp into sps_update_beagle_jar

github-actions · 2025-11-25T15:34:42Z

Remember to squash merge!

github-actions · 2025-11-25T15:34:53Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

github-actions · 2025-11-25T15:34:54Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
ImputationBeagle.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

github-actions · 2025-11-25T15:37:47Z

Remember to squash merge!

github-actions · 2025-11-25T15:37:58Z

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
All WDLs and changelog files appear to be valid for this release.

github-actions · 2025-11-25T15:37:59Z

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

jsotobroad

looks good, can you link the warp-tools PR in the description of this doc so we can reference it if need be.

jsotobroad · 2025-11-25T15:52:13Z

tasks/wdl/ImputationBeagleTasks.wdl


    java -ea -XX:MaxRAMPercentage=90.0 -XX:MinRAMPercentage=90.0 -XX:-UseCompressedOops \
-    -jar /usr/gitc/beagle.17Dec24.224.jar \
+    -jar /usr/gitc/beagle.d820c4e.jar \


oh man this si gonna be so much better moving forward with provenance

jsotobroad · 2025-11-25T16:05:53Z

pipeline_versions.txt

 IlluminaGenotypingArray	 1.12.26	2025-10-09 
 Imputation	 1.1.23	2025-10-03 
-ImputationBeagle	 2.3.0	2025-11-12 
+ImputationBeagle	 2.4.0	2025-11-25 


i think this is fine, patch would have been fine too since there is no "actual" changes to the output but your reasoning is very valid.

mmorgantaylor · 2025-11-25T18:34:48Z

pipeline_versions.txt

 IlluminaGenotypingArray	 1.12.26	2025-10-09 
 Imputation	 1.1.23	2025-10-03 
-ImputationBeagle	 2.3.0	2025-11-12 
+ImputationBeagle	 2.4.0	2025-11-25 


yeah I like the minor version change here

mmorgantaylor · 2025-11-25T18:35:18Z

pipelines/wdl/arrays/imputation_beagle/ImputationBeagle.changelog.md

+2025-11-25 (Date of Last Commit)
+
+* Update Phase and Impute tasks to use a docker image that contains Beagle JAR 
+generated from GitHub repo [tmp-sharing/imp-server](https://github.com/tmp-sharing/imp-server/tree/master).


man I wish this repo wasn't called tmp-sharing 😬

update beagle docker image for testing

ba26e46

use image from base-version branch

e3eea8b

use image with different git command

614a2c5

salonishah11 mentioned this pull request Nov 20, 2025

[TSPS-682] Update Beagle Dockerfile to build jar from Github repo broadinstitute/warp-tools#176

Merged

use image with git hash in dockerfile

2824304

correct beagle jar name

43b9d07

use version 2.0.0 docker image

555a92c

update changelog and versions file

7ab2019

salonishah11 changed the title ~~[DO NOT MERGE] [TSPS-682] Update beagle docker image~~ [TSPS-682] Update beagle docker image Nov 25, 2025

Merge branch 'develop' into sps_update_beagle_jar

d911678

salonishah11 force-pushed the sps_update_beagle_jar branch from 1c37e85 to d911678 Compare November 25, 2025 15:20

Updated pipeline_versions.txt with all pipeline version information

002995a

salonishah11 commented Nov 25, 2025

View reviewed changes

salonishah11 added 2 commits November 25, 2025 10:33

commit to get GHA running

dbbd2fb

Merge branch 'sps_update_beagle_jar' of https://github.com/broadinsti…

fa4866c

…tute/warp into sps_update_beagle_jar

update pipeline version in main wdl

447bec3

salonishah11 requested review from a team, jsotobroad and mmorgantaylor November 25, 2025 15:39

jsotobroad approved these changes Nov 25, 2025

View reviewed changes

mmorgantaylor approved these changes Nov 25, 2025

View reviewed changes

[TSPS-682] Update beagle docker image #1722

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salonishah11 commented Nov 17, 2025 •

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