Correct directory for files I'm ftp'ing for galaxy?

Naive question: I can ftp files into my GVL instance but I’m not sure where to put them for Galaxy to see them? Can anyone help please?

I can’t help I’m afraid Claire, but I would also like to be able to do this!!!

Hi both,

Galaxy uses its own data/file structure to store data files, so the process is a little more than just copying files into a directory.

First, you need to make sure you are set as the admin user (you can add your galaxy login email address to the list of admin users on the cloudman ‘admin’ page).

Once you have done that, you should be able to follow this tutorial:

to import your directory of data on your server, into galaxy.

You will need to follow the instructions for ‘Upload files from filesystem paths’ - as that is the mechanism by which Galaxy can import data from the filesystem on the system where it is running. I have checked, and all of the config options should work, though if you run into problems let us know and we will try to help!

Best wishes,


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This took a bit of puzzling (I’ve never used Galaxy!), but it works like this.

  1. Sign up as a galaxy admin via {instance ip}/cloud. Once you sign up Galaxy restarts, which takes a bit of time, so don’t panic if the Galaxy section of your dashboard has a red cross next to it briefly.

  2. Create a Galaxy account at {instance ip}/galaxy. Click User>Register, enter the email address you used above and a secure password.

  3. From the Tools panel in Galaxy, select Upload File and then click “Chose FTP file”. This will display an error because we haven’t FTP’d anything yet, but it does give the details for how to do so.

  4. Open your FTP client of choice (WinSCP, FileZilla, etc) and enter the instance ip address as the host, and the email address and password of the Galaxy user you created in step 2.

  5. Upload files >2Gb into that directory specifically.

  6. Close the “Choose FTP file” dialog and re-open it.

  7. Tick the uploaded files and click start.

Please bear in mind that this can only be done on newish GVL instances, because of the issue we had with Cloudman recently.

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Great, thanks @mattbull, thanks @tom!