Yes, I can confirm that the indexing is still not functioning. I dug a bit deeper and the tool package is likely going to stay deprecated, despite the legacy wrappers being hosted at the EU server. I put some more comments on the ticket at the EU site. The developers will see it and either close it out or let us know if things change.
What to do for now
Try using currently supported methods instead.
- Salmon, Kallisto, or StringTie can be used to quantify transcripts or isoforms.
- DESeq2, limma-voom, or edgeR are available for DE analysis after.
- IsoformSwitchAnalyzeR can be used after quantification for even more exploratory work.
The GTN tutorials linked above incorporate most of these tools, and each has some additional Help resources linked down on the tool form. If you run into problems, this forum has lots of existing help and you can ask about anything not yet clarified.
Suggested places to start would be
- Hands-on: De novo transcriptome reconstruction with RNA-Seq / De novo transcriptome reconstruction with RNA-Seq / Transcriptomics
- Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics
Not all tools have a demonstration tutorial in Galaxy, but tools work the same in Galaxy as anywhere else! That means you can use a publication’s methods, and then topics here can help with dovetailing into the downstream tools that do happen to be covered in a tutorial.
- You can find tool Q&A by searching here or see the bottom of tool forms. As an example, these are linked on the Salmon tool form and cover items like getting reference data prepared.
I know this isn’t the answer you wanted but I hope it helps to clarify what is going on and what the other current choices are! 