I'm having difficulties uploading a local GTF file into a local instance of galaxy. I'm using the Data Library upload through Shared Data then Add datasets to current folder from path. Once uploaded in to the Data Library I import the file to my history. The file looks like it imports correctly. However, when I look at the file it shows one line of data and the rest of the data is in the comments section. Additionally, the file shows "Required metadata values are missing." when you click the edit option.
Note: This does not happen if I get data from UCSC directly to my history share it in the data library and import it back into history. All data is in the line sections that way and usable.
Does anyone have any insight into what is happening here and how to correct?
Well that is interesting; disregard my comment on updating then. Which library dataset are you importing? Could you please link it? Also could you please share that history with us (send the link to galaxy-bugs@bx.psu.edu )?
On usegalaxy.org my PI uploaded via the get data upload file tool and acquired the 1 line multiple comments history. The shared data library data tool was used when we use our local instance of galaxy. Is there a way to provide you the GTF since the file is not uploaded into the data libraries on the main galaxy host?
I am still unable to reproduce, I tried this on UCSC-obtained gtf file and the whole round of importing into library and then to history works well to me. At this point I suspect that your gtf file in the library is somewhat abnormal. Can you please link it?
Here is the link to the history. I'll email it to the suggested email as well. Trying to find a way to link the gtf file for you atm. Also, I had no trouble acquiring the data from UCSC to my history --> uploading it into a library --> importing back into history. My trouble came about when I acquired the data from UCSC into my history --> saved the file locally on my node --> loaded the file into the data library --> imported the file to history, or when I uploaded a self curated GTF file into the library and so on. History
I downloaded the file from UCSC to my machine, then FTP transferred to Galaxy and import directly into library and then to history -> I think that covers your case.
Thanks for the history. Interestingly enough the number of comments stays the same even if I recalculate the metadata on it, which means the metadata script is not correct. However I was able to run a job on the file and it handled it correctly (ran it on all lines, ignoring the metadata saying they are comments)
I created an issue for it here: https://github.com/galaxyproject/galaxy/issues/2298
Thanks for creating an issue Martin. Also, I attempted to run a cufflinks job on an annotation file upload that way and it failed. However, it worked with the same annotation file straight from UCSC.