Add postgres singularity option #1492
Merged
Conversation
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
|
Uh, that is cool! Nice to see planemo used in this way. |
|
Can you fix the linting failures ? |
absolutely! |
Smeds
force-pushed
the
add-postgres_singularity-option
branch
3 times, most recently
from
1eac873 to
408ba7c
Compare
…tainer as database when running planemo.
Smeds
force-pushed
the
add-postgres_singularity-option
branch
from
408ba7c to
985e237
Compare
|
@mvdbeek I think I managed to fix the linting errors. |
|
Thanks @Smeds! |
mvdbeek
reviewed
Jul 9, 2025
| self.database_user, | ||
| self.database_password, | ||
| self.database_host, | ||
| self.database_port, |
There was a problem hiding this comment.
@Smeds It looks like we never expose the port from the container ... how does this actually work ? In my hands I see the container run and the data directory gets created and all, but then it tries to connect to localhost and fails:
sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) connection to server at "localhost" (::1), port 5432 failed: Connection refused
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
Hi!
I’ve been experimenting with running Planemo on the TACC server using SLURM, and I ran into an issue where more complex workflows would fail due to the SQLite database being locked.
Since I don’t have the ability to launch a Docker container for database access on TACC, nor access to an external database, I developed a solution: running a PostgreSQL database within a Singularity container. However, I wanted to avoid manually starting the Singularity container each time. This pull request introduces functionality that allows Planemo to automatically launch a Singularity instance for the PostgreSQL database and stop it once the workflow completes (or fails).
While I’m unsure if this feature will be useful to others, it was extremely helpful during my testing with Planemo.