Question: sub history in Galaxy
1
gravatar for ranav001
4.0 years ago by
ranav00110
Israel
ranav00110 wrote:

Can I create a sub-history (sub-directory) in Galaxy.

I may be running several projects - each having its own files organized in histories.

I want to keep each project in a separate main history.

Usually, when I finish a project I delete its histories (backing it up first on my computer) so that I will have all my resources available for the next project.

Yet, this time I might use data from project A in conjunction with data from project B.

Some of these data files are fairly large and it would make my life tolerable to keep both projects (for a while) in Galaxy but in 2 different "main" histories.

Thanks

Ran

ADD COMMENTlink modified 4.0 years ago by Jennifer Hillman Jackson25k • written 4.0 years ago by ranav00110

Do I understand it correctly that you are trying to solve a problem with having not enough space for your project?

ADD REPLYlink written 4.0 years ago by Martin Čech ♦♦ 4.9k

Hi Martin,

 

No, I have enough space since I remove all histories once a project is completed.

My need is for ease of managing, say, two projects simultaneously - sharing the same data files.  And doing this without putting the files of both projects in the same history.

Ran

ADD REPLYlink written 4.0 years ago by ranav00110

I will also add a comment here. If you are working on a local or cloud Galaxy, and have "admin" privileges, datasets that are under frequent usages can be added to 'Shared Data -> Data Libraries'. This is a good choice for reference datasets (not reference genomes, or perhaps for smaller ones that you do not intend to index as a native resource). 

You may also be able to work with your administrator to create libraries that are of use to multiple users on the same Galaxy instance. Data copied out of a library also does not contribute to an individual account's data quota usage. This is good for Galaxy administrator's and for users.

Although this is generally not possible on the public Main Galaxy instance (the creation of new libraries - we do try to keep this resource at a minimum - to keep access simple) - you can publish a history, include it in a "Page", publish that, then multiple users (everyone on the same instance) would be able to to copy the history/datasets contained for analysis.

Hopefully combined these two answers help you to find a solution that will help in the immediate term.

Best! Jen, Galaxy team

ADD REPLYlink written 4.0 years ago by Jennifer Hillman Jackson25k
0
gravatar for Bjoern Gruening
4.0 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi Ran,

this is, to the best of my knowledge, not possible currently.

Please create a Trello card: https://trello.com/b/75c1kASa/galaxy-development so the Galaxy team can track this feature request.

Cheers,

Bjoern

ADD COMMENTlink written 4.0 years ago by Bjoern Gruening5.1k

Thanks Bjoern.  I'll do that.

Ran

ADD REPLYlink written 4.0 years ago by ranav00110
0
gravatar for Jennifer Hillman Jackson
4.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Just to add to the above for usage now ...

If a dataset is in one history, and you copy it over into another history (within the same account), this will not increase your data quota usage. The copy is just that - a copy - underneath it is technically a reference to the original dataset.

Many tools have been or will be expanded in the near term to permit the selection of datasets from multiple histories and from data libraries (much how a Trackster visualization will permit an accounts/server data "source" browsing in a pop-up window). 

Until then, this is the way to go. Best, Jen, Galaxy team

ADD COMMENTlink written 4.0 years ago by Jennifer Hillman Jackson25k

Thanks Jennifer,

I am really not concerned about quota as I always remove all histories when a project is done.  And, while working on a project, I remove files that served their purpose (usually saving them first to my disk).

The thing is - organizing files such that less time and energy is spent on looking for something I have already done and more on thinking about meaning.

The ability to create sub-histories will be of great help on that.

Ran

 

ADD REPLYlink written 4.0 years ago by ranav00110
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