Opened 15 years ago
Last modified 15 years ago
#218 assigned task
Proof-of-concept: run a selected GenePattern module from BASE
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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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 by , 15 years ago
Status: | new → assigned |
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comment:2 by , 15 years ago
comment:3 by , 15 years ago
(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 by , 15 years ago
comment:5 by , 15 years ago
(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.
(In [1110]) References #218: Proof-of-concept: run a selected GenePattern module from BASE
It works! But...