Can I Merge Histories?

7.5 years ago by

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Curtis, Instead of merging histories, merge the datasets back together by using the download and upload tools. Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

ADD COMMENT • link written 7.5 years ago by Jennifer Hillman Jackson ♦ 25k

Jen Thanks, that works, mostly. All the task numbers are now changed, but not updated in the names of tasks. Additionally, I don't see any way to identify the input tasks aside from the names that were generated. Again, I've lost by trace back ability. If I look in the "info" the "names" of the input files are incorrect, and if I generate a workflow, everything is connected incorrectly. If you are not familiar with this bug, I can reproduce it on the public server, if you want. I will certainly use that copy-dataset feature to maintain one clean history with my source data, and copy it into my working histories, but doesn't seem to work for merging histories. Regards, Curtis To: Robert Curtis Hendrickson Cc: 'galaxy-user@lists.bx.psu.edu' Subject: Re: [galaxy-user] can I merge histories? Hello Curtis, Instead of merging histories, merge the datasets back together by using the download and upload tools. Hopefully this helps, Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

ADD REPLY • link written 7.5 years ago by Robert Curtis Hendrickson • 130

Jen, Thanks for all your quick responses. I have found Googling documentation for Galaxy extremely hard, because it is such a common term. How I wish it had been misspelled (intentionally)! I work in an informatics core, where several of us collaborate on projects. We have a local Galaxy installation. We are working hard to become proficient at Galaxy as we get deluged with NGS analysis requests. We recently tried to have two of us work in the same history, but did not succeed. I "shared" the history with my colleague, but he was un-able to use it directly. If he "imported" it or "cloned" it, it made a copy. Even when he "referenced" it, any new tasks he ran did not show up in my original history. I see there are a bunch of roles under history > options > "dataset security", but I haven't been able to figure out how to use them, or if they would help with this issue. We currently use Shibboleth for authentication, and have no groups or roles defined. I'm not currently an admin, but that will get fixed shortly. Is there a specific tutorial or page that covers this type of collaborative setup? I looked at https://bitbucket.org/galaxy/galaxy- central/wiki/SecurityFeatures, but still wasn't clear if I could achieve what I want with roles and groups. Regards, Curtis

ADD REPLY • link written 7.5 years ago by Robert Curtis Hendrickson • 130

Hi Curtis, It may be helpful if I first help to clarify how the history/dataset/workflows are organized. 1 - When a dataset is moved (through either method), internal linkage is not preserved. You could resolve this in two ways: a - By annotating where the moved result dataset came from. One suggestion for this would be to add in name of the other history - unique history naming would be advised - and keeping that history around for reference/traceability. b - Putting all of the work in the same history (best solution, especially if you are going to be creating workflows) 2 - When a history is shared, the other user creates a clone of your history as it exists when it is first imported by them. To conserve space, the underlying datasets are kept as a single file on the file system (as long as they are unchanged), but no user accessible linkage exists between the two histories after the clone is created. Changes in one history do not effect the other. If you want to share new results, have your collaborator import the history again. Naming imported histories in some way that will distinguish between revisions would be a good idea (unique names for histories is advised, shared or not). 3 - There are no roles that will allow two users to actively work on the same history. Also, it is not recommended to share the same user/password in an attempt to work in the same space - unexpected results may occur (not bugs, just internal tracking conflicts). Hopefully this helps to address your questions about sharing histories, but please let us know if something was missed or is still unclear. For searching the Galaxy wiki, specificity can be achieved by using a site key plus the search term. This is the Google link with the Galaxy wiki site key included. After clicking into Google with this link, add in your search term(s) after the site key and submit. http://www.google.com/search?q=site%3Ahttp%3A%2F%2Fbitbucket.org%2Fgal axy%2Fgalaxy-central%2Fwiki This link is also documented at the very bottom of the Galaxy wiki home page: https://bitbucket.org/galaxy/galaxy-central/wiki/Home Thanks for using Galaxy! Jen -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/

ADD REPLY • link written 7.5 years ago by Jennifer Hillman Jackson ♦ 25k

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