Send galaxy-user mailing list submissions to galaxy-user(a)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(a)bx.psu.edu You can reach the person managing the list at galaxy-user-owner(a)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(a)gmail.com&gt; Subject: Re: [galaxy-user] Workflow improvement requests (long) To: "Assaf Gordon" <gordon(a)cshl.edu&gt; Cc: galaxy-user(a)bx.psu.edu Message-ID: <15d850bd0811250314h4075f1edld1ea2dc6b1a76fef(a)mail.gmail.com&gt; 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(a)cshl.edu&gt;: > 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(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user > > ------------------------------ _______________________________________________ galaxy-user mailing list galaxy-user(a)bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user End of galaxy-user Digest, Vol 29, Issue 16 *******************************************