Proof-of-concept: run a selected GenePattern module from BASE

[Nicklas Nordborg]

It doesn't matter much which module that we choose, but it is preferrable if the module can be used with the regular test data. One suggestion is to use the ComparativeMarkerSelection module which is used in the tutorial: ​http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_tutorial.html

[Nicklas Nordborg]

(In [1110]) References #218: Proof-of-concept: run a selected GenePattern module from BASE

It works! But...

• There is very little error handling.
• There is no integration with exporters.
• File selection must be made manually. The default choices made by BASE are poor.
• Results files are imported back to a child bioassay set. There is not much to do with them except to look at them in a text editor.
• Lots of other possible enhancments... for example aborting a job...

[Nicklas Nordborg]

(In [1119]) References #218: Proof-of-concept: run a selected GenePattern module from BASE

Now uses a custom JSP page with some more interaction. Uses the new wrapper classes.

[Nicklas Nordborg]

(In [1128]) References #222, #218, #229. Several changes just to make things work.

[Nicklas Nordborg]

(In [1131]) References #218: Proof-of-concept: run a selected GenePattern module from BASE

Changed file transfer code and error handling so that stderr.txt is actually loaded into BASE. This concludes the major parts of the plug-in. It should be possible to run any GP module/pipeline. User-friendlyness is a remaining issue. Everything sent to GP must be in a file and there is very little logic for finding/creating input files. Results are also only stored as file and can't be imported as new spot data.