Hi, I’m trying to run AnnotateMyIDs but I get this error; please what does it mean? and what should I do, I am still a beginner.
/corral4/main/jobs/046/311/46311947/tool_script.sh: line 9: R: not found
/corral4/main/jobs/046/311/46311947/tool_script.sh: line 10: Rscript: not found
Update 11/16/2022
The indexes are restored at UseGalaxy.org. Prior failed runs should now complete successfully.
Thanks to all who reported the issue for their patience!
Hi @Nahla_OUARD
Technically, this means that the tool did not have any valid input to send to sub-functions the tool is executing. This can be due to input problems or a transient cluster issue.
If you are actually working at UseGalaxy.org (I see a bug report about this same issue) – the built-in annotation for this tool and the upstream Featurecounts tool is an open known issue we are still working on. The problem started about 3 weeks ago, and will likely not be fixed until later next week. I’ll mark this topic for an update.
You can try at UseGalaxy.eu or UseGalaxy.org.au instead for now OR supply a reference annotation GTF from the history instead of using the built-in annotation.
Hi @jennaj, thank you for your answer.
Yes, I am working with usegalaxy.org and I did have a problem with the gene annotation file, so I uploaded it from the internet. I don’t know if its correct to do that or not. I am working on mm10.
Please, is there any other tools in galaxy that I can use to do the annotation beside annotatemyids. thanks in advance
You can use this exact tool at a different public Galaxy server. It looks like you already know how to transfer data by URL. That will work between servers for individual files (set the history to a shared state first) or you can transfer entire histories, too. FAQ transfer-entire-histories-from-one-galaxy-server-to-another.
Other tool options should show up in the tool panel with a keyword search for “annotate”. One example that uses an external GTF’s content is deg_annotate.
The final option is to get whatever annotation that you want to link in into a tabular format and join it with your current data based on common matching identifiers, or even overlapping genomic regions. How to do this isn’t exact but several types of general text and coordinate-based manipulations are covered in the GTN’s Intro tutorials.
One of those should work out for you 
Oh thank you, I really appreciate your help