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pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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LIB functionality not working #7

Closed tstoeger closed 9 years ago

tstoeger commented 9 years ago

filepathsep =

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Custom project code support is enabled by temporary expanding of MATLAB path by including all the subfolders under: /BIOL/sonas/biol_uzh_pelkmans_s7/Data/Users/RNAFish/IndividualExperiments/150430_mycHprtRescan/JoinedHprtMycRescan/LIB/MATLAB {Undefined variable "labrep" or class "labrep.createPath".

Error in brainy.libpath.checkAndAppendLibPath (line 12) projectMatlabPath = labrep.createPath(libDir, {});

Error in PreCluster_with_pipeline (line 7) brainy.libpath.checkAndAppendLibPath(OutputPath); }

ewiger commented 9 years ago

It should be fixed now. I have just tested that CPCLuster function can recognize and pick up code in LIB/MATLAB

>> CPCluster('/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/150331_HCT116_DS1_CC/BATCH/Batch_data.mat','/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/150331_HCT116_DS1_CC/BATCH/Batch_1012_to_1016.mat');
CPCluster - 12:40:14: Starting CPCluster
CPCluster - 12:40:15:   batchfile = /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/150331_HCT116_DS1_CC/BATCH/Batch_data.mat
CPCluster - 12:40:15:   clusterfile = /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/150331_HCT116_DS1_CC/BATCH/Batch_1012_to_1016.mat

filepathsep =

/

Custom project code support is enabled by temporary expanding of MATLAB path by including all the subfolders under: /BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/150331_HCT116_DS1_CC/LIB/MATLAB
CPCluster - 12:40:27: Analyzing image set 1012 (max threads = 1)
CPCluster - 12:40:27:   01: LoadImages 
CPCluster - 12:40:29:     Image set 1012 = 150331_HCT116_DS1_CC_D04_T0001F004L01A01Z01C01.png
CPCluster - 12:40:29:   02: IlluminationCorrectionZScoring 
Applying illumination correction on channel number: 1