Hi, so I’ve completed my analysis in Galaxy and now when I try to download a list it never initiates. I can download the individual files, but when one has over 700 results to download individual files can be rather tedious. I’ve tried generating both rocrate.zip and a tar.gz compressed files but when I open the dataset folder none of my file names are included which presents another issue.
Renaming files:
As stated previously, both compressed file types generate braken reports that do not contain the original file name which makes it relatively difficult for me to continue with statistical analyses if I can’t map the samples. I’ve tried writing an R script to read the data_attr.txt file and match it to files in the datasets folder to no avail. S.O.S Please send help.
Cheers~
Hi @zpho3nix
There are a few ways to download data.
-
Export the entire history preserving the directory (collection folder) structure. Do this under History 
→ Export History to File.
-
Export just some of the files by either copying them into a new history and exporting that, or use the 
on datasets or with the download link on a collection.
I just re-tested those methods, and the datasets retained the original names.
But I’m guessing that what you want is the sample name instead, yes? The original data had a sample name that was later processed. That result dataset doesn’t have the sample name anymore.
If that is true, then I would strongly recommend using collections and possibly a workflow for your processing.
For this part
This is the download link on the collection folder method, correct? I noticed that this was taking a while to start up (and complete) at UseGalaxy.eu today. The server is likely busy but this did work for me. Maybe try again?
For large data and slower connections, exporting the history to a file, then moving data by URL to other cloud environments will likely work faster.
Then for this part
If you run the data through in collection folders, the element identifiers of the original sample files will be persistent throughout the analysis. There are also strategies that involve tags. You can also custom file rename inside of a workflow.
Details are here → Using Galaxy and Managing your Data / Tutorial List. But you can also use some of these tools to work with what you have now and possibly rename the existing result data. A tool like Apply rules might be enough but it is hard to guess without seeing the data.
If you would like to share a history or some screenshots, and explain how you want to relabel, we can try to help more. Data is never stuck in a particular shape and renaming should be possible.
Let’s start there, thanks! 
Hi jennaj, thanks for your efforts but I just downloaded and renamed all the files manually over a period of days. None of the above solutions were applied, but I appreciate your time.
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