I second the request on sometype of labeling system for the workflow--at least a numbering system. I made a workflow with many inputs, then when I tried it out I realized that the first input that I was joining with the second input was intermixed and unidentifable. Then I realized that the inputs are ordered in their creation order and not anytype of order how they are placed. Since I was making many, many, inputs I simply made a bunch of them at once and didn't keep track of their order or where I put them.

Thank again for the sweet tool.


On Tue, Nov 25, 2008 at 12:00 PM, <galaxy-user-request@bx.psu.edu> wrote:
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Today's Topics:

  1. Re: Workflow improvement requests (long) (James Casbon)


Message: 1
Date: Tue, 25 Nov 2008 11:14:14 +0000
From: "James Casbon" <casbon@gmail.com>
Subject: Re: [galaxy-user] Workflow improvement requests (long)
To: "Assaf Gordon" <gordon@cshl.edu>
Cc: galaxy-user@bx.psu.edu
Content-Type: text/plain; charset=ISO-8859-1

Hi Everyone,

Slightly off-topic, but I see you have awk in your workflows.  Awk
could work on text, tabular, and other formats but I'd rather not
define a new tool for each input type.

Is there a way to define a tool which accepts more any type of input?
It should ideally preserve the format in the output as well.


2008/11/14 Assaf Gordon <gordon@cshl.edu>:
> Dear all,
> Recently, users (of our local galaxy server) started using workflows, and
> are very pleased. However, as workflows get more complicated, it gets harder
> to track the input and output of the workflows.
> I'd like to share an example, to illustrate the problems that we encounter.
> The workflow (pictured in the attached 'workflow.jpg') takes 4 input
> datasets, and produces 4 output datasets.
> The first problem is that there's no way to differentiate between the input
> datasets (They appear simply as "Step 1: Input dataset", "Step 2: Input
> Dataset", etc). Since each dataset has a specific role, I've had to print
> the workflow and give the users instructions as to which dataset (in their
> history) goes into what dataset. (see attached
> 'crosstab_workflow_input_datasets.jpg').
> The second problem is that whenever I change something in the workflow and
> save it - the order of the dataset change!
> So what was once dataset 1, can now be dataset 2,3 or 4.
> Users have no way of knowing this... (keen users might notice the the
> description of the first tool changed from "Output dataset 'output' from
> step 2" to "Output dataset' output' from step 4" - but this is very
> obscure...).
> The third problem is that once the workflow completes, the resulting dataset
> have cryptic names such as "Join two queries on Data 10 and Data 2". Since
> "Data 10" is "Awk on Data 8" and data-8 is "Generic Annotations on Data 7
> and Data 1" and data-7 is "Intersect data 1 and data 6" - it gets a bit hard
> to know what's going on. (see attached 'crosstab_history.png').
> For the meantime, I've simply gave written instructions on what each dataset
> means (see attached 'crosstab_workflow_dataset_explnanations.jpg).
> If I may suggest a feature - it would be great if I could name a dataset
> inside the workflow. Instead of naming it "Input dataset" I could give it a
> descriptive name, so even if the order of the input datasets changes, users
> will know which dataset goes into which input.
> Regarding the output dataset names, the 'label' option in the tools' XML is
> a good start, but still creates very long, hard-to-understand names.
> Another great feature would be the possibility to add an 'output label'
> for each step in the workflow.
> Regardless of the above, I'd like to say (once again) that Galaxy is a great
> tool, and workflows are really cool - we have several long workflows which
> do wonderful things.
> Thanks for reading so far,
>   Gordon.
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user


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End of galaxy-user Digest, Vol 29, Issue 16

Eric M Schauberger
Physician Scientist Training Program (DO/PhD)
Genetics Program
Ewart Lab
MSU College of Osteopathic Medicine (MSUCOM)
Email: Schaube2@msu.edu
Skype: Emschaub
See my availability: http://www.timebridge.com/mytime/eschauberger