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
Adhemar, This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on 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. 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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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>
Adhemar,
This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on 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. 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:
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> Adhemar,
This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on 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. 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:
I already tested and it's working like a charm. Thank you very much Dannon. -Adhemar 2011/12/19 Dannon Baker <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> Adhemar,
This was a bug that has been fixed as of changeset 6368:de03f821784b, which should be available on 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. 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 (2)
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Adhemar -
Dannon Baker