transfer history from my account on one Galaxy server to another Galaxy server

history
share-or-publish
download
upload
workflow

#1

Hi. I want to transfer a history that someone shared with me. I imported it into a Galaxy account I had on one server (temporary- as part of a class I did). Now I want to import it into my regular Galaxy account. I tried using the email option, but then it says I can’t transfer to myself, so then I tried creating and copying the URL, but nothing appears in my Histories or Shared Histories. I used Import from File to do this - wrong way? Thanks.


#2

If the server is still up and public, or you have downloaded the history archive, then moving the history to another server is possible.

You state that the accounts are on different Galaxy servers. This is why the share by email didn’t work. To share with another user by email, both accounts must be on the same server. All accounts on the same Galaxy server will have distinct registered email addresses.

Galaxy FAQs:

Options for Data Sharing

Loading/Downloading Data

Tips:

  1. Make sure the history is set as “Shared” at the original server. This is required.
  2. Click on the link in the archiving message (blue box) to get an updated status until noted as being completed and ready for import/download. The larger the history, the longer it will take the archive to build. Permanently deleting any data not needed will make the history smaller and the archive creation faster.
  3. Once the archive is ready, clicking on the link a second time will launch a download dialogue (where to save it, etc). This can be dismissed if you are not going to download it. Copy the URL instead for a direct Galaxy-to-Galaxy transfer.
  4. You can navigate away from the export page and do other thing while waiting (including logging out). But be sure to watch it, archived histories remain on servers for a set length of time (varies by the server, generally about a day or so).
  5. If clicking on “Export to File” starts the archive creation again instead of taking you back to the original archive already in progress, the server might not support archive creation or you may have waited too long to check back.
  6. Downloading a history archive locally from one server, then uploading it to another, works for almost all cases regardless of firewalls and other server configuration. If transferring by URL fails, try that instead. Keeping a backup of your work is a good idea anyway, plus these archives can be uncompressed to use the included datasets for other purposes.

#3

Hi Jennifer,

Thanks for your reply. I have still not been able to transfer to my other Galaxy server account, although I did save the diagram of the workflow and captured the text from View Workflow, so I have some record.

When it says below to set the history as Shared, where is this? I tried going to Share or Publish under settings, and have tried Share with User or Make accessible and Share Link without success, but did not select Make Accessible and Publish, as the original workflow was not my own.

I also tried Download History and saved it as a file that I then tried to Import to my other Galaxy account, but nothing actually appears when I upload the file.

Am I missing something obvious here?!

Thanks,

Bruce


#4

Yes, the sharing just needs to be by a link. You don’t need to publish.

You also seem to be confusing Workflows and Histories but that might be just how I am reading your comment. To be clear: these are distinct objects. Each have similar Share/Publish options, covered in an FAQ under here (the first one).

  • For a History: under Saved Histories – click on a history name for a pull-down menu that includes Share or Publish. Or if that history is currently loaded, find that same option in the history panel menu (gear icon). Histories .tgz archives are imported from the history menu with Import from File (but both “file” and “URLs” are accepted on the form).
  • For a Workflow: option is under Workflow ( top masthead item, the result page is named “Your Workflows”) – click on a workflow name for a pull-down menu. Workflows have a button on that same listing page (top right corner) for importing/uploading the .ga files.

Please be aware of this newer feature: When sharing a history, you have the option of just sharing the history or also sharing the objects (eg: datasets) so others can work with them. Unshare to see which you picked, and check on the “also share objects” and recreate the share link if needed.

The FAQ needs an update to include all this, and we might need a new one for importing. I’ll take care of that. The UI was changing quite a bit this year and will again in the next release, then it should be stable for a bit longer again.

If the above as all been done, let’s troubleshoot more from this info from you:

  1. What server are you trying to upload the Galaxy history archive to? URL please, or state if not public (your own Galaxy? Version? Source?)

  2. Are you using the function under History menu > Import from File?

  3. Is the file you are trying to load a History archive (ends with .tgz) and not a Workflow file (ends with .ga)

  4. Does the history archive actually contain data? Check the file size and uncompressed/review contents as needed. It will be about the same size as the original history in the browser (this info is displayed at the top of the history panel, or on the saved history listing).


Mpileup with vcf output? How to change galaxy to older version?
#5

Hi Jennifer,

Thanks for your reply.

I think where I went wrong before is that although I did download a file with data in it, I did not also click on the link show below, but went straight to import my downloaded file in the destination Galaxy. I have tried a few times and it seems that clicking on the link below, and then importing by Archived History Link is working better for me than import from Archived History File (also with the link below clicked). I hope this makes some sense, but either way, I now have both of the files I need transferred.

For completeness, here are answers to your earlier questions…

  1. https://usegalaxy.org/

  2. yes

  3. The file is tar.gz

  4. yes

Thanks for all your help!