Question: Why does Galaxy use a 'history' and not a 'directory' to manage user content?
1
gravatar for steve
19 months ago by
steve30
NYC
steve30 wrote:

Why was this implementation chosen, at least on the front-end if not on the back-end as well? I understand that files in a user's History are currently contained as a blob in a database (correct?). Does this have an advantage over simply storing it as plain files in a user-directory created by Galaxy? Is there any plan to implement a "directory view" on the front-end to manage history files easier when the history grows very large?

In the context of my own use cases, a lot of our current pipelines are very 'file-oriented', so the prospect of trying to get them implemented in Galaxy seems a little daunting.

ADD COMMENTlink modified 19 months ago by James Taylor470 • written 19 months ago by steve30
3
gravatar for James Taylor
19 months ago by
James Taylor470
United States
James Taylor470 wrote:

While Galaxy stores metadata about a dataset (name, datatype, tags) in its database, the data are actually stored in files on disk. This is what makes it possible to integrate existing command line tools that alrady work on files.

The history is one view of a set of files in Galaxy that corresponds to the order in which analysis steps were performed. Datasets can also be viewed in a hierarchical "Data Library".

We do not store the file in a user's directory because datasets in Galaxy can be shared by many users.

ADD COMMENTlink written 19 months ago by James Taylor470

OK thanks, I see the page about this here. I have poked around and found some of the files I've generated in Galaxy here: /galaxy-central/database/files/. One of my concerns is that non-admin Galaxy users will be requesting downstream analysis (outside of Galaxy) on files they have generated within Galaxy. Is there an easy way for them to find the direct paths to their files so that our non-Galaxy Bioinformaticians can easily access the files on the server? Hoping to avoid unneccessary import/export of data in Galaxy if we can just access it directly from the file system. EDIT: Just found that clicking 'View Details' on a History item does show the full path.

ADD REPLYlink modified 19 months ago • written 19 months ago by steve30
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