Hello, I am trying to use RNA-STAR but I don’t believe the proper drosophila genome annotation is available under “built-in reference genome”. The two options are DM3 and release 6 ISO1 MT. However, I am looking specifically for DM6. Please let me know if I am missing something. I am using my own GTF files I obtained from flybase.
Best,
Max
Any annotation will always be based off a specific version of a reference genome. Using anything different will lead to issues between the coordinates in the BAM versus the annotation file. The built in reference genomes are only for convenience. Pairing up a genome and annotation source, loading both into Galaxy, and using them together is really common!
Your FlyBase annotation likely has a header that describes the genome assembly version it is based on. You can probably source this genome fasta from the same place that you obtained the annotation. If you would like to share the header lines back here, or the GTF file as loaded into a shared Galaxy history, we can help you to locate the correct fasta, or help to confirm the fasta you have already loaded is the correct version!
This FAQ has a short description of the custom-genome process. → FAQ: How to use Custom Reference Genomes?
You could also decide to source this data from NCBI, this is how. → FAQ: NCBI reference data
Or, UCSC will have both files too in their Downloads area. → UCSC Genome Browser Downloads.
Please let us know if you have any questions or need help locating files. We’ll need to know where you want to source these from first! 
Hey jennaj, thank you for information. Here is the header from the GTF files. For the assembly, I am using the 6 ISO1 MT built-in index provided by galaxy. I have tried removing the first 4 lines of the GTF file but I am still getting an error. Should I try downloading the GTF and FASTA files from NCBI and retrying? Or is there a way I can reformat the GTF file?
Your annotation file appears to be from the same genome assembly as the built in index. That means you should be able to use it after some data preparation.
You are correct about the extra header lines. Please try remove them to see if that is enough.
Then, if you are getting an error or some odd result, you are welcome to share back the log message or better, the history, for some feedback.
unfortunately I think I am getting a new error after using a FASTA and GTF downloaded from the same NCBI webpage. No idea what the issue is. What is a good email for you so I can share my history?
actually here is a link if that makes things easier: /usegalaxy.org/api/short_term_storage/0e0ab561-ac87-40e8-9e1f-e9ed94bced35
I sent you a direct message where you can share your history. I’ll watch for your reply! We’d like to get this going for you!
UseGalaxy.org had a cluster issue later last week that may have resulted in jobs failing very quickly. We had a cluster allocation expire and a few jobs slipped through before we could reroute away.
These failures will likely not have detailed logs or messages. Instead, to learn if your job was impacted, click to expand one of the red outputs datasets to find:
Remote job server indicated a problem running or monitoring this job.
Please try a rerun now!
If these failures impacted your workflow run, remember to see the extra options on the tool form to replace collection elements and resume workflow dependencies.
See the GTN tutorial example showing how to use the rerun function to correct a job. → Hands-on: Introduction to Galaxy as an RDM platform / Introduction to Galaxy as an RDM platform / Introduction to Galaxy Analyses (# re-run-a-tool)
Resume and Replace explained with screenshots! → Rerunning only failed jobs in a workflow: Replace and Resume functions
@Maksym_Dankovskyy I’ve replied to your direct message. The reference data looks very good! The failure was due to a problem on our side. A rerun should be enough.
Thank you for the follow-up and our apologies for the confusion! If errors persist for anyone, we can troubleshoot more. 
