I was trying to download all my large collections to clear out spaces for my next analysis. But all download failed no matter when using Chrome or curl command, my browser said incomplete files and curl just closed transfer with nothing downloaded (and I tried using APIs as suggested in the tutorial but still same). The message shows as below:
Can someone help me out? I thought this could be network problem but I tried different places and different time point, still not working.
Two items to check first, and one alternative method:
Downloading datasets using command line
Try downloading one collection at a time.
The alternative is to export a history archive, and download that. The files will be in a folder inside the archive after uncompressing it. The process is the first part of this FAQ. If your collections are very large, consider putting each in a distinct history, and archiving/downloading that way in smaller data chunks. Transfer entire histories from one Galaxy server to another
If you need more help, please confirm the URL of the server where you are working. Actually UseGalaxy.org?
Thank you for the information, I have successfully download datasets using history archive. However, I want to know more infos about the direct downloading using browser, which started failing every time after the galaxy getting updated, no matter what datasets and browsers I choose. I do download one collection each time, and I think it is much more convenient than using history archive, especially for large number of files so I don’t have to rename each of them. And for your information, I used usegalaxy.org all the time. Would you like to help me out?
The collection download functionality at UseGalaxy.org (and only that server) is undergoing some updates. Details: Download collection broken fails with "file incomplete" · Issue #15390 · galaxyproject/galaxy · GitHub
For now, exporting a history is the most reliable method.