Question: How to save sequence data and analysis results outside of Galaxy
1
gravatar for Politz, Samuel M.
15 months ago by
Politz, Samuel M.70 wrote:

I have some important data and an entire analysis of the data saved on Galaxy since 2013. I don't have a local instance of Galaxy. Is there some way I can save everything locally so that I can put it back into Galaxy if I need to work on it again or document the results? I still have the raw data files offline but my workflow is complex and I wouldn't want have to solve all the problems again by repeating the whole thing. Thank you.

assembly alignment galaxy • 535 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by Politz, Samuel M.70
1
gravatar for Martin Čech
15 months ago by
Martin Čech ♦♦ 4.6k
United States
Martin Čech ♦♦ 4.6k wrote:

Try History Options / Export History to File. This will give you link to a tarball that has all the datasets and metadata in it. Can be imported back into Galaxy at later time.

ADD COMMENTlink written 15 months ago by Martin Čech ♦♦ 4.6k
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

Both the primary History menu and the primary Workflow menu have options for downloading an archive of the content (for backup and/or later transfer into Galaxy again).

This means that the history and the workflow can be saved as local files that do not need to be loaded into a local or cloud Galaxy. Even though active content (not deleted or perm deleted) is retained indefinitely at this time at Galaxy Main (http://usegalaxy.org), we recommend that any important data is backed up, the same you would for any analysis - within Galaxy or not.

At Galaxy Main, you have the choice of leaving your data (history and/or workflow) at Galaxy Main as active after downloading a copy as a local backup. Again, leave the content as active to ensure it is retained. It does not need to be deleted/permanently deleted unless you need space for new work. History content counts toward your user account quota but Workflows do not (at this time and it is not a planned change).

Other public Galaxy servers have different data retention policies - contact the server admins of that instance if it is not declared in their help/support content to find out what that is and to avoid losing important work. Or contact them to double check anyway, if you do not save local archives files of the work.

There are more details about this, but let's start here. For example, some users will create a local or cloud instance that contains the exact tools and Galaxy version used for the original analysis to ensure exact reproducibility, since Galaxy Main will change over time, sometimes requiring tool updates or other workflow edits. Even though there are guided processes to aid with this upon upload of an older archive, and reproducibility is a primary goal for the Galaxy project, sometimes changes are necessary and the results may not be what you want/need later on. A Docker container is one way to create a static Galaxy configuration that exactly matches the environment the original analysis was done with - and works best when done right after an analysis is finalized, yet can be done after. The galaxy-dev@lists.galaxyproject.org has much prior Q&A about how to create and use a Docker container to backup a usable working environment, allowing for exact reproducibility over time.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 15 months ago • written 15 months ago by Jennifer Hillman Jackson25k
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