On Tue, Nov 25, 2008 at 12:00 PM,
<galaxy-user-request@bx.psu.edu> wrote:
Send galaxy-user mailing list submissions to
galaxy-user@bx.psu.edu
To subscribe or unsubscribe via the World Wide Web, visit
http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
or, via email, send a message with subject or body 'help' to
galaxy-user-request@bx.psu.edu
You can reach the person managing the list at
galaxy-user-owner@bx.psu.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-user digest..."
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
Message-ID:
<15d850bd0811250314h4075f1edld1ea2dc6b1a76fef@mail.gmail.com>
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.
thanks,
James
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
>
>
------------------------------
_______________________________________________
galaxy-user mailing list
galaxy-user@bx.psu.edu
http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
End of galaxy-user Digest, Vol 29, Issue 16
*******************************************