Hi Mike,
I have been making use of the workflow feature in Galaxy and I think it is an excellent way to make use of the tools and share analyses with others. Recently I have noticed that some of steps within the workflow have been disconnected due to tool changes.
"Problems were encountered loading this workflow (possibly a result of tool upgrades). Please review the following parameters and then save."
Which tools have been problematic for you? We've been upgrading some of the 'operate on genomic intervals' tools, specifically Intersect and Subtract, recently to accommodate GFF files as well as BED-like files. These tools should be stable now.
A week ago I reconnected the workflow steps yesterday found that some step were disconnected. I corrected this yesterday and was able to save and test it. Today however I have returned to the workflow and the again several of the connections between functions have been lost. I was planning on using and publishing a link to this workflow (i.e. for a manuscript). Is this a good idea or is it still a beta function which will not be stable? I have a bit of a complex workflow and I am not sure if it is a good idea to continue to repair it? Any feedback on how one should work with the workflows would be great.
We can't make any promises, but many tool wrappers are stable and the workflow infrastructure should definitely be usable for production/publication. Also, you can watch our development repository to see if we've recently made changes to particular tools: http://bitbucket.org/galaxy/galaxy-central/changesets/
An alternative idea is to run your own Galaxy instance with the tool versions that you need so that you can be confident that your published workflow is stable.
Perhaps one nice feature would be a way to freeze/lock-down a workflow so it will run inspite of future Galaxy updgrades (in addition to having a more plastic one that evolves along with the upgrades). Also a way to export the workflow in a meaningful way would be useful as it can be difficult to remember all the step once the links are broken.
Freezing a tool or specifying a particular tool version to run is something we'd like to do, but it's not high on our development list right now. Exporting workflows is much higher on our list but is still in development. One idea for now is to take a screenshot of your workflow so that it's easier to reconnect when tools change and you to need to reestablish connections.
Thanks, J.