I’m trying to use an RNA-seq pipeline to analyze my own data for C. elegans.
Every time I try to upload the gtf file download from UCSF, wormbase, or ensemble, I get the following error message “An error occurred setting the metadata for this dataset”.
After one day trying different options on solving the problem, I have tried to upload the same dataset on the galaxy.eu in which I did not receive any error. This made me to think that there is no problem with the file itself.
May I ask if there is a bug on
the galaxy.org my local Galaxy server and if it’s possible to fix it?
Thank you so much!
could you share your history with me? I’ll have a look at it.
thank you so much for replying to me and to have a look at it.
Here is the link for the history.
Please let me know if it’s not working as it is my first time sharing it.
Line 169 is the metadata error, and in line 168 I tried to use the auto detection to correct it, but it’s running since yesterday.
Any advice you would have, I will really appreciate it.
Thank you so much!
it seems that you are using a local Galaxy instance. Could you run the analysis in usegalaxy.eu? In that way, I could have access to your history.
Yes, I can.
Even though in the galaxy.eu I didn’t have any error.
Galaxy | Europe | Accessible History | rna-seq
It is line1. I did as a trial to know whether the problem was associated with the file. I’m not sure if this information can be useful. If there is an additional way I can try to run the analysis without using the local Galaxy.
I just found out that if I upload the same gtf file on the galaxy without using the local server (using .org or .eu), there is no metadata error detected.
How could I fix it when using the local one?
Did you or anybody encounter a similar problem?
Data upload problems are usually the first indicator of some configuration problem after a new Galaxy is first started up.
That said, sometimes odd errors, including this one, are produced when a file is not completely uploaded (new server or not). There could be many reasons for that with a local Galaxy server. A local Galaxy needs some admin configuration to be used without problems coming up. Some of this we can help with and some of this will be specific to your computer/network that we can’t help with (since it is private) but we do have documentation that covers the basic setup and use cases.
There will be a training event in March that includes administrative topics. Many of the tutorials linked above will be included. Anyone can join. The event is global, asynchronous, and many more people from the community will be available to help. GTN Smörgåsbord 2: 14-18 March | Gallantries
You can also go through those tutorials on your own now and try to uncover the problem, or at least be able to provide more context about your configuration so the community can assist here. Examples of information that will help: Galaxy version, computer OS/version, dependency management choice(s), what admin configurations you have done, plus how some tests worked out. Have you installed tools and run tool tests? The goal is to find out things like: Do other datasets load properly? This same file type fails (always/sometimes? from different sources or just one particular source?). Do other data upload successfully – or do all uploads fail? Has any upload ever worked? Have any tools ever worked? If the analysis was successful before, have you made any changes since things worked?
What may be best if you do not want to go through all the administrative setup/tests, and this is a new server that you haven’t heavily invested in already:
Try an alternative deployment choice. Docker Galaxy comes with more of the administrative details pre-configured. Details here: Galaxy Docker - Galaxy Community Hub
Problem solved after re-installing the Galaxy!!
Thank you so much for the help!!