Dear All, I used to work with galaxy web site gladly, until I need to apply one workflow with (tens of join operations) on tens of datasets. so the problem is that if I need to run the workflow, each time I need to indicate the input datasets for each join operation and that is not interesting at all, and very time consuming. "although they are the same for each input file, in theory what I need to change is only the main input file, and leave the other files of the join operations the same, sound easy :)". I have read the comments for the "Workflows & Multiple datasets" post, on "how to run a workflow for multiple input files", and its now only working on galaxy-central, which I downloaded and used and it works fine and will solve one side of my problem the remaining will be with the fixed part inside the workflow. One last comment: the folder uploading functionality in galaxy-central is not working properly with me, the process continue until running the "uploading commands" but the files are all with 0 size, the same process on galaxy-dist works well... Much appreciated, heba --- Heba Saadeh Ph.D. Student Dept. of Medical and Molecular Genetics, Medicine School, King's College London, Guy's Hospital, 8th floor Tower Wing, London, SE1 9RT. Office: +44(0)20 7188 3715 ________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Adhemar [azneto@gmail.com] Sent: 19 December 2011 18:35 To: Dannon Baker Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Workflows & Multiple datasets I already tested and it's working like a charm. Thank you very much Dannon. -Adhemar 2011/12/19 Dannon Baker <dannonbaker@me.com<mailto:dannonbaker@me.com>> Ahh, I should have specified, that changeset is in the galaxy-central repository and has not been moved to galaxy-dist yet. I think we're testing a few more things, but this should happen in the near future, at which point you could simply update from galaxy-dist as usual, or you could pull directly from galaxy-central right now if you'd like. -Dannon On Dec 19, 2011, at 12:50 PM, Adhemar wrote:
Dannon, Thanks for the immediate reply. I just retrieved the latest code from the repository and it's not working
$ hg summary parent: 6298:b258de1e6cea tip
I also tried 'hg pull -u -r 6368:de03f821784b' but it says:
pulling from https://bitbucket.org/galaxy/galaxy-dist abort: unknown revision '6368:de03f821784b'!
How or when can I update to the release you mentioned? Thanks, -Adhemar
2011/12/19 Dannon Baker <dannonbaker@me.com<mailto:dannonbaker@me.com>> Adhemar,
This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on main.g2.bx.psu.edu<http://main.g2.bx.psu.edu> in the near future. If you're running a local instance, you'll find this resolved as soon as you update to that changeset or higher.
Unfortunately, there isn't a fast way to copy datasets into a data library from multiple histories at once. I think you might find it faster to use the standard "Copy Datasets" functionality in the history Options menu to move everything you'd like into a single new history, and from there move it into a library. This Copy Datasets action allows you to select an individual history to copy from, instead of manually changing to the history first, so it should save you some time to do it that way.
-Dannon
On Dec 19, 2011, at 12:12 PM, Adhemar wrote:
Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20
The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well?
I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'?
Thank you, Adhemar
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://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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Hi Heba, I wanted to follow up on this. Apologies, but I became a bit lost about where this problem is occurring. Is this in your local install, using a galaxy-central pull? When was the last pull? Is the problem resolved now? Curious to know if this is something we need to be aware of as an open issue or not. If so, I'd like to have it clarified and open a bitbucket ticket to track a (potential) future correction. Any specific details that you could provide would be appreciated (including a use case or public history/workflow shared link). Thank you for the feedback! Jen Galaxy team On 12/20/11 4:24 AM, Saadeh, Heba wrote:
Dear All,
I used to work with galaxy web site gladly, until I need to apply one workflow with (tens of join operations) on tens of datasets. so the problem is that if I need to run the workflow, each time I need to indicate the input datasets for each join operation and that is not interesting at all, and very time consuming. "although they are the same for each input file, in theory what I need to change is only the main input file, and leave the other files of the join operations the same, sound easy :)".
I have read the comments for the "Workflows& Multiple datasets" post, on "how to run a workflow for multiple input files", and its now only working on galaxy-central, which I downloaded and used and it works fine and will solve one side of my problem the remaining will be with the fixed part inside the workflow.
One last comment: the folder uploading functionality in galaxy-central is not working properly with me, the process continue until running the "uploading commands" but the files are all with 0 size, the same process on galaxy-dist works well...
Much appreciated, heba --- Heba Saadeh Ph.D. Student Dept. of Medical and Molecular Genetics, Medicine School, King's College London, Guy's Hospital, 8th floor Tower Wing, London, SE1 9RT.
Office: +44(0)20 7188 3715 ________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Adhemar [azneto@gmail.com] Sent: 19 December 2011 18:35 To: Dannon Baker Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Workflows& Multiple datasets
I already tested and it's working like a charm. Thank you very much Dannon. -Adhemar
2011/12/19 Dannon Baker<dannonbaker@me.com<mailto:dannonbaker@me.com>> Ahh, I should have specified, that changeset is in the galaxy-central repository and has not been moved to galaxy-dist yet. I think we're testing a few more things, but this should happen in the near future, at which point you could simply update from galaxy-dist as usual, or you could pull directly from galaxy-central right now if you'd like.
-Dannon
On Dec 19, 2011, at 12:50 PM, Adhemar wrote:
Dannon, Thanks for the immediate reply. I just retrieved the latest code from the repository and it's not working
$ hg summary parent: 6298:b258de1e6cea tip
I also tried 'hg pull -u -r 6368:de03f821784b' but it says:
pulling from https://bitbucket.org/galaxy/galaxy-dist abort: unknown revision '6368:de03f821784b'!
How or when can I update to the release you mentioned? Thanks, -Adhemar
2011/12/19 Dannon Baker<dannonbaker@me.com<mailto:dannonbaker@me.com>> Adhemar,
This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on main.g2.bx.psu.edu<http://main.g2.bx.psu.edu> in the near future. If you're running a local instance, you'll find this resolved as soon as you update to that changeset or higher.
Unfortunately, there isn't a fast way to copy datasets into a data library from multiple histories at once. I think you might find it faster to use the standard "Copy Datasets" functionality in the history Options menu to move everything you'd like into a single new history, and from there move it into a library. This Copy Datasets action allows you to select an individual history to copy from, instead of manually changing to the history first, so it should save you some time to do it that way.
-Dannon
On Dec 19, 2011, at 12:12 PM, Adhemar wrote:
Hi, I was searching for how to run a workflow for multiple input files and I was very happy to find it's already implemented as mentioned here: http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20
The problem is that it's not working for me. When I select two files, for example, it runs the workflow only in the first file. Even if I check 'Send results to a new history', it only creates a new history called 'test 1' and not the others. Is my instance somehow misconfigured or it's happening to others as well?
I'm also looking for a way to add datasets to a library from different histories. Do I really need to open each history one by one and use 'Import datasets from your current library'?
Thank you, Adhemar
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org<http://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:
___________________________________________________________ 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/wiki/Support
participants (2)
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Jennifer Jackson -
Saadeh, Heba