Question: Issues with importing Galaxy History to another Galaxy server
1
gravatar for negin_valizadegan
9 months ago by
negin_valizadegan10 wrote:

Hi,

I ran out of space in Galaxy Main and need to analyze more data, but I don't want to loose my initial data and completely delete it. Since my histories have lots of big files, it is very furstrating to download each file separately. Also, each file has two download options bi and bam and I am not sure which one I need for importing these to Galazy again if I need at some point in the future. I am fine with storing these to my hard drive as well but again downloading large files one by one is the problem. I tried exporting history and allowed it to be shared but the step for importing it to another Galaxy server does not work. I just see the sign that it is importing but nothing happend the whole day. Any hints would be much appreciated!

Thanks, Negin

ADD COMMENTlink modified 9 months ago • written 9 months ago by negin_valizadegan10
1
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Testing Update:

I can confirm that downloading/uploading a History archive is not functioning in Galaxy version 17.09, which is the most current release. Transferring data by URL has worked. Just be aware that the history must be shared ("accessible by a link" is enough, it does not need to be "published" too) and the archive must be fully ready before starting the import (click on the given history archive link, or go back to "History menu > Import History from File" until it states "Ready").

A ticket tracking some earlier issues with these functions was still open so I added in a new comment about this problem for our development team to review and correct. Please follow for updates: https://github.com/galaxyproject/galaxy/issues/3235#issuecomment-358805440

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k

Do I need to update my Galaxy version or would it be updated automatically?

Update: Nevermind. I found mine is current.

ADD REPLYlink modified 9 months ago • written 9 months ago by negin_valizadegan10
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Few item to check:

  1. Are the histories you are exporting marked as being accessible by a link? This is one of the History Sharing options. This is noted in help text of the first result page after choosing the option to Export to File. Set this before attempting to download an archive or to import it from the link: https://galaxyproject.org/learn/share/

  2. It takes some time to build the archive. Meaning, it can not be used immediately, especially for large histories. For a large history, wait for the archive to be ready. Re-clicking on Export History to File will give status.

  3. Be aware that if your data contains collections, those will not be exported. This is a priority enhancement in progress. There also used to be a problem if all datasets did not have distinct names - but I haven't tested that recently. If all else fails and you have duplicated dataset names, try making them different.

  4. When loading a BAM dataset to Galaxy (any method), only the bam, not the bam.bai is needed since a new index is created upon upload to the server.

  5. If using a link to import continues to fail, I would be curious if downloading the file and then uploading it would have a different result. It is recommended to keep a local downloaded archive of your work anyway.

I have a simple export/import test running to double check there are no new problems server-side. More feedback once complete.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 9 months ago • written 9 months ago by Jennifer Hillman Jackson25k

Hi Jen,

Thank you for your detailed response. Answers to your comments below:

  1. My history is accessible.
  2. I waited to the archive building to be complete. I used it when it was complete.
  3. What do you mean from collections? I am not sure what it means. Dataset names are each different from each other.

Thank you for your explanations regarding 4 and 5.

Best, Negin

ADD REPLYlink modified 9 months ago • written 9 months ago by negin_valizadegan10
0
gravatar for negin_valizadegan
9 months ago by
negin_valizadegan10 wrote:

The problem still persists. I wish Galaxy had more memory.

ADD COMMENTlink modified 9 months ago • written 9 months ago by negin_valizadegan10
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