RetroPath2.0 fails to run and retrosynthesis workflow reports missing rpTools dependency

usegalaxy.org support
,
1

Hello,

Since yesterday, I have been unable to run RetroPath2.0 on the GalaxyBioCAD online interface (https://galaxy-synbiocad.org/). The tool starts but fails during execution with generic exit code errors. The standard error output shows that the KNIME workflow fails to load due to a missing chemistry data type:

ERROR	 main Node	 Loading model settings failed: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.
org.knime.core.node.InvalidSettingsException: Data cell implementation 'org.knime.chem.types.SmartsCell' not found.

In addition, when attempting to run the retrosynthesis workflow, Galaxy reports that a required tool is missing:

Workflow cannot be executed. Please resolve the following issue:
Following tools missing:
toolshed.g2.bx.psu.edu/repos/tduigou/rptools_rpextractsink/rptools_rpextractsink/6.5.0+galaxy0

Are these tools and dependencies correctly installed and available on the server, or have there been recent changes affecting RetroPath2.0?

Thank you very much for your help.

2

Welcome @alola

Yes, there could be a problem with a tool update, or some event on the server itself impacting the jobs.

We can’t confirm this at the forum but we can help to direct you to the correct contact.

Try sending an email to the administrative support contact to report the issue. You can include a link to this topic for context (and potential updates!). Consider also including a link to a shared history with the error job (this makes review faster).

Alternatively, you can send in a bug report directly from the error dataset, then put the extra context into the comment area. Bug reports with meaningful comments tend to be reviewed with priority!

I hope this helps and please let us know what happens! :slight_smile: