Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Load test data in sda #19

Merged
merged 7 commits into from
Jun 18, 2024
Merged

Load test data in sda #19

merged 7 commits into from
Jun 18, 2024

Conversation

MalinAhlberg
Copy link
Member

@MalinAhlberg MalinAhlberg commented May 7, 2024

This PR adresses part 1 of #4 .

When starting the gdi containers, data from #17 is loaded to the sensitive data archive. Instructions for downloading it can be found here and instructions on how to access it via htsget can be found here.

For info of the binary sda-cli see this repo (version used).

@MalinAhlberg MalinAhlberg changed the title Feat/use test data Load test data in sda May 8, 2024
@MalinAhlberg MalinAhlberg requested a review from wna-se May 8, 2024 09:30
@MalinAhlberg MalinAhlberg marked this pull request as ready for review May 8, 2024 09:30
Base automatically changed from feat/add_test_data_b1mg_demonstrator to main May 21, 2024 14:18
@@ -25,7 +25,7 @@ services:
healthcheck:
test: curl -fq http://localhost:9000/minio/health/live
restart: no
ports: !override []
# ports: !override []
Copy link
Member

Choose a reason for hiding this comment

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

I would keep this or remap the ports to expose them here instead, ideally with an environment variable to be able to configure the external port. E.g.,

    ports: !override
      - ${PORT:-1234}:1234

Copy link
Member Author

Choose a reason for hiding this comment

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

yes, sorry, this was just intended for testing, but happened to be commited. Reset in 01bd15d

Copy link
Member

@wna-se wna-se left a comment

Choose a reason for hiding this comment

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

Works well! Might be useful to also load the BAM file used in the containerised compute example.

@MalinAhlberg
Copy link
Member Author

Might be useful to also load the BAM file used in the containerised compute example.

Sure. Or do we have any bam file more related to this project?

@MalinAhlberg
Copy link
Member Author

MalinAhlberg commented Jun 4, 2024

I created #26 for adding a more interesting bam file.
@wna-se please approve this PR when you are happy with it.

@MalinAhlberg MalinAhlberg merged commit bb50b74 into main Jun 18, 2024
@MalinAhlberg MalinAhlberg deleted the feat/use_test_data branch June 19, 2024 06:58
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants