Changes between Version 8 and Version 9 of Modules/Compute/UsingRscripts

Timestamp:

2011-02-24T18:43:48+01:00 (14 years ago)

Author:

Morris Swertz

Comment:

--

Modules/Compute/UsingRscripts

@@ -80 +80 @@
 
         //define what other 'compute protocol' MOLGENIS should call (obviously the one we defined above)
-        submitJob(command="OneTraitQtlMapping", genotypes_name=genotypes_name, phenotypes_name=phenotypes_name, traitnames=selectedNames);
+        submitJob(protocol="OneTraitQtlMapping", genotypes_name=genotypes_name, phenotypes_name=phenotypes_name, traitnames=selectedNames);
 
         //Note: all parameters you pass to submitJob will be automatically passed to the other protocol
@@ -97 +97 @@
 ||number_of_jobs ||Integer ||This will determine how the phenotype dataset will be split in jobs; should be 1 or larger. ||
 
+== user story: using the job submission API to create 'anonymous' compute applications ==
 
->>Discussion: we could even decide here to generate a whole R script and pass that as the command. How cool would that be? Than the other protocol doesn't even have to exist in the database.
+How to demo:
 
+In the above use story we used the job submission API to start pre-existing compute protocols (in this case, !OneTraitQtlMapping).
+However, we can also create a variant where the job is a script instead of a protocol (aka, an 'anonymous protocol'):
+
+{{{
+
+//here our script will use the job submission API so you can run many R scripts
+for(i in 1:number_of_jobs)
+{
+        //cut out a subset of the phenotypes
+        selectedNames <- sliceList(i,number_of_jobs)
+
+        //define what other 'compute protocol' MOLGENIS should call (obviously the one we defined above)
+        script <- paste("genotypes <- getFromDb(genotypes_name)",
+                             "phenotypes <- getFromDb(phenotype_name)",
+                             "onetraitqtlmapping(trait_names, genotypes, phenotypes)", sep="\n")
+        submitJob(script=script, genotypes_name=genotypes_name, phenotypes_name=phenotypes_name, traitnames=selectedNames);
+
+        //Note: all parameters you pass to submitJob will be automatically passed to the other protocol
+        //result is that a new "computeapplication" will be created programmatically instead of via the UI to be sent to the cluster
+}
+
+}}}
+