Remove Sanger S3 URL from Pf8#1233
Merged
jonbrenas merged 2 commits intomalariagen:masterfrom Apr 1, 2026
Merged
Conversation
jonbrenas
approved these changes
Apr 1, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Changes in this commit
With migration away from Sanger infrastructure we need to remove URLs to Pf8 data stored on Sanger's S3 system, leaving only URLs to GCS.
I have:
pf8_config.jsonand replaced with GCS URL as defaulttests/integration/test_pf8.pyTesting run
test_pf8.py: 16/16 checks passedOnce this is approved / merged, default S3 access will be removed for Pf8 users. Access to S3 data is still possible with specifying a URL, e.g.
malariagen_data.Pf8('s3://pf8-release/snp-only/')as long as the data are on S3.I have also created a PR to update Pf8 data access guidance here: malariagen/parasite-data#77 which can be merged once these changes are approved.