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-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Adhemar [azn...@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<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.

-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<dannonba...@me.com<mailto:dannonba...@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



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___________________________________________________________
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