Cron scripts on test and main will need to be updated when the server is.
GOPS complement tool and annotation profiler will now correctly use chromosome lengths files if available.
and tools. Moved some methods related to params out of the Tool class, sets
of inputs can also be used in other ways (e.g. for modules). More abstraction
needed here.
is "InputDataset" which allows a workflow to have an input dataset which many
different tools can use (without needing to specify it repeatedly. Still need
to extract out a common interface (tools will become another type of "module")
which will clean this up a lot.
properly update the 'terminals' for the nodes in the editor. Many other fixes
to saving and loading of workflows (error tracking should now be working
properly).
the workflow editor. Some improvements from workflow pushed back to main
interface. IE specific CSS and javascript tweaks removed. No longer relying
on 'quirks mode' to make things work (instead, relying on IE7.js to make IE
behave like a standards compliant browser).
every page can be added to galaxy.base.js). Cleaned up history templates
accordingly. Also, added scripts from IE7.js which fix many layout bugs in
older versions of IE.
to drop the `stored_workflow` table if you have it before running this).
Much better separation between the underlying model and the json model used
to communicate with the browser. Various interface improvements. Most things
should work properly now (excepting still dynamic options and input
parameters inside groupings).
a link to workflow management from the tool menu. From there new workflows
can be created and existing workflows edited / run.
Still substantial problems with:
- Selects using "dynamic options" of any sort
- Repeat/conditional tools (no way to connect inputs in a repeat or conditional)
The database / json representation is a real mess. I'm going to completely
redo that next.
connections
2) Added a script for packing the javascripts, everything is now repacked
with yui-compressor (the packed versions are slightly large, but they
gzip better resulting in an overall reduction).
Daniel Blankenberg