Update 2023-03-07
File naming issue resolved. Use version 3.13.0+galaxy2 or later.
Hi @Ashikha @Cosmo @Ola_Alessa
Roary is one of the few tools that interprets dataset names by necessity. Most other tools don’t – metadata like the datatype, or the actual dataset contents are used instead.
Workarounds that tend to solve most issues with weird results from this tool are listed in the issue ticket here: Roary 3.13.0 fails at usegalaxy.org -- likely installation issue · Issue #293 · galaxyproject/usegalaxy-playbook · GitHub
If those don’t work for some reason, we would definitely like an example in a shared history link. A small public example is best as we might want clone it to include in that ticket’s workaround or reassess whether any part of the issue can be addressed. And if the tool is actually silently failing for suspected resource reasons with larger data/stricter params, an example would be helpful. Post the shared link here as a reply (public), or ask @gallardoalba or me to start up a private message to share it in (if not shared already!).
Every example of odd failures or odd outputs I’ve reviewed was not dependent on the number/size of inputs – all were dataset naming issues. But that could be a biased set. While it is certainly possible to create a really massive computationally expensive job that fails to produce results at a public site (could happen at one or multiple – each uses different resources), those usually result in “red” error results. Very few produce empty (putatively successful) “green” results, and I don’t think that is a known yet about this particular tool.
Thanks in advance for the feedback!