Opened 12 years ago

Last modified 12 years ago

#218 assigned task

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

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: ZZ GenePattern integration v1.0
Component: net.sf.basedb.genepattern Keywords:
Cc:

Description

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

Change History (5)

comment:1 Changed 12 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 12 years ago by 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...

comment:3 Changed 12 years ago by 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.

comment:4 Changed 12 years ago by Nicklas Nordborg

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

comment:5 Changed 12 years ago by 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.

Note: See TracTickets for help on using tickets.