Add postgres singularity option#1492
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mvdbeek merged 3 commits intogalaxyproject:masterfrom Mar 5, 2025
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Uh, that is cool! Nice to see planemo used in this way. |
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Can you fix the linting failures ? |
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absolutely! |
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…tainer as database when running planemo.
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@mvdbeek I think I managed to fix the linting errors. |
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Thanks @Smeds! |
mvdbeek
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Jul 9, 2025
| self.database_user, | ||
| self.database_password, | ||
| self.database_host, | ||
| self.database_port, |
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@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
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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.