Folks, Is there some way I can merge histories? I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and contrast it. Thanks, Curtis
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 On 6/14/11 9:36 AM, Robert Curtis Hendrickson wrote:
Folks,
Is there some way I can merge histories?
I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and contrast it.
Thanks,
Curtis
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
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 -----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Tuesday, June 14, 2011 11:53 AM 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 On 6/14/11 9:36 AM, Robert Curtis Hendrickson wrote:
Folks,
Is there some way I can merge histories?
I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and contrast it.
Thanks,
Curtis
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/
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
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%2Fgalaxy%2F... 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/
Yes, you can copy datasets from one history to another. In the history panel, click "Options", and then "Copy Datasets" to do so. -Dannon On Jun 14, 2011, at 12:36 PM, Robert Curtis Hendrickson wrote:
Folks,
Is there some way I can merge histories?
I ran a workflow on 3 different samples in one history, each time putting them in a different history with the same name. However, Galaxy created 3 new histories, each with the same name! But I need the data in the same history to compare and contrast it.
Thanks, Curtis
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
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Dannon Baker -
Jennifer Jackson -
Robert Curtis Hendrickson