Hi!
This is my first time using galaxy, and I’m really struggling to upload large files that are to big to upload as local files.
My files are saved locally.
I tried using FileZilla to use FTP to upload files but it won’t conncet to the server.
I’ve tried zipping them which worked when I try to upload them but galaxy says they’re txt files and I can’t seem to convert them in galaxy.
I tried to compress to gzip.
I tried directly using command line, but it never worked.
Any ideas??
Hi @Renee02,
What kind of data do you have? How big are the files?
Galaxy supports GZipped versions of some (many?) datatypes. Support for multi-file archives is rather minimal, plus, multifile archive might be very big. If GZipped version of format is supported by Galaxy, use GZipped files.
Many Galaxy servers do not support upload by ftp anymore.
If you are on a fast network, upload of files in GB scale should not be an issue.
Kind regards,
Igor
Its all FASTQ files, around 3-8 GB. I tried GZipping, and it would show blank files everytime it uploaded. The uploading them locally took forever but it does work, I’m just hoping for an alternative.
Hi Renee02,
I do not expect any issue with upload of 3-8 GB files to the ORG sever over web interface. The file sizes are standard for FASTQ files. However, I strongly recommend GZipped FASTQ files over plain text FASTQ: compressed files are usually five times smaller, and Galaxy can handle GZipped FASTQ files.
Try upload of a single file. Drag and drop a file into Galaxy upload menu.
With rare exceptions, data upload issues are caused by external factors, not Galaxy, hence, hard to identify. Do you know your upload speed? Are the files on your computer or on external storage? Do you use wireless or LAN (blue cable) connection? Are you based in the US? If not, maybe try other public Galaxy servers, such as Galaxy Europe.
What do you mean by a blank file after GZipping? Do you get an empty file after compression or after upload to Galaxy? Are you Mac OS or Windows user? On Mac you can compress (GZip) a file using Terminal. On Window, 7-Zip was a good option.
Use a single file archives (compress individual files).
Kind regards,
Igor
Hopefully this is working now! 
We have another method for those who prefer to work on the command line. And @igor is correct – this all works about the same for someone moving data up from their own computer. The limit is usually the internet speed of the computer where the data is coming from.
Most UseGalaxy.* servers now support the galaxy-upload tool as far as I know. It works through the API and the script is local to your computer.
Loading data up to a 3rd party cloud source then moving it over to a public Galaxy server from there, then the archive result sent back to your cloud storage, is another really nice choice if you want to only have to *get the data up into the cloud" one time or expect to have really large results. Galaxy archives are just compressed directories, and can be navigated to pick out individual files if the 3rd party service supports uncompression from tza. (On your own computer this is always possible, but maybe not at all cloud storage providers).
What connections are supported differ by server. Check under your account User > Preferences to see the currently available options. Some are under Manage Information and others might be in the other views linked on that top level view.