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
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
Dept. of Medical and Molecular Genetics,
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[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Adhemar [azn...@gmail.com]
Sent: 19 December 2011 18:35
To: Dannon Baker
Subject: Re: [galaxy-user] Workflows & Multiple datasets
I already tested and it's working like a charm.
Thank you very much Dannon.
2011/12/19 Dannon Baker <dannonba...@me.com<mailto:dannonba...@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.
On Dec 19, 2011, at 12:50 PM, Adhemar wrote:
> 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?
> 2011/12/19 Dannon Baker <dannonba...@me.com<mailto:dannonba...@me.com>>
> 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.
> 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
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The Galaxy User list should be used for the discussion of
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