I have set up Mercurial to fetch updates from galaxy-dist, and it seems that my version of galaxy is up to date.

- Should I pull from galaxy-central to get this update (7057:08fbfeaaf3e1)?
- If so, could you please tell me how I do that?
- Do you know how I permanently change repository from galaxy-dist to galaxy central, without loosing my tools and modifications?

Kind Regards

- Frank

Den 18-04-2012 14:09, Dannon Baker skrev:
Hi Frank,

This should be resolved as of changeset 7057:08fbfeaaf3e1.  Thanks!


On Mar 27, 2012, at 4:37 AM, Frank Sørensen wrote:

Hi Dannon,

Unfortunately our server is (still) behind a firewall, so I can't share 
anything, but I hope you can reproduce the error from the following description.

If I make a vanilla test workflow say:

Input Dataset ->  Map with BWA for Illumina (single end) ->  SAM-to-BAM ->  

and save it. Then all outputs will show if I run it, even if none of the 
"snowflakes" are checked which is not logical. It would be better if the output 
visibility was checked by default, and the user should actively de-select the outputs 
that should be hidden, but that's another matter.

If I edit the workflow that I just created, and select the output from flagstat 
to be visible, then the two other (BWA and SAM-to-BAM) will be hidden when I 
run it, which they should be. So far so good...

If I edit the workflow again and select the remaining outputs (BWA and 
SAM-to-BAM) to be visible and save the workflow, then only BWA will be visible 
after run, thats a problem, SAM-to-BAM should also be visible since that's what 
I selected.

If I want the output from SAM-to-BAM to be visible, I have to edit the workflow 
again, and de-select visibility of the output from SAM-to-BAM, save the 
workflow, and re-edit the workflow and select visibility of the output from 
SAM-to-BAM and save the workflow.

It seems that selection/de-selection of output visibility only works under some 
circumstances and not others.

I can conclude the state of the output visibility on the existing or missing post-hide-action, 
which is apparent if I select "run workflow", and press "expand all" on the 
Running workflow screen, so I don't actually have to run the workflow, which is a great help.

By tweaking my workflows using this editing / re-editing method, it is actually 
possible to get the visibility of all outputs into the state that I desire, but 
it is quite cumbersome on larger workflows.


- Frank

Frank Sørensen, B.Sc., Programmer
Molecular Diagnostic Laboratory (MDL)
Molekylær Medicinsk Afdeling (MOMA)
Århus Universitetshospital Skejby, Brendstrupgårdsvej, 8200 Århus N
Tlf. +45 7845 5363
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