Executable, run_CoMIK shell script and the performMKLShogunPython M-f…

…ile updated to correct for an error due to which mkl.py could not be successfully run.
snikumbh · Aug 1, 2017 · cd34d92 · cd34d92
1 parent 9b8bc81
commit cd34d92
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Showing 4 changed files with 4 additions and 2 deletions.
diff --git a/CoMIK b/CoMIK
diff --git a/README.md b/README.md
@@ -39,7 +39,7 @@ comik_wrapper('config-comik.txt');
 ./run_CoMIK.sh <MATLAB_Runtime_location> <config_file>
 ./run_CoMIK.sh /usr/lib/matlab-9.0 config-comik.txt
 ```
-where `/usr/lib/matlab-9.0` is the typical location of the MATLAB runtime on a Linux machine.
+where `/usr/lib/matlab-9.0` is the typical location of the MATLAB runtime on a Linux machine. If required, you can add your own paths to the `LD_LIBRARY_PATH` environment variable in the file `run_CoMIK.sh`.
 
 
 _CoMIK_ requires two FASTA files as input -- the first FASTA file containing sequences in the positive class; the second FASTA file containing negative class sequences. Other params are explained below.

diff --git a/performMKLWithShogunPython.m b/performMKLWithShogunPython.m
@@ -102,7 +102,7 @@
 predLabels = zeros(size(Ytest));
 subkernelWeights = zeros(nKernels,1);
 %
-cmdToRunPythonScript = ['mkl.py -K ', trainkernelfilesListFilename, ' -Y ', trainlabelsFilename, ' -C ', num2str(Cval), ' -P ', num2str(mklNorm), ' -O ', predLabelsFilename, ' -T ', testkernelfilesListFilename, ' -L ', testlabelsFilename, ' -I ', num2str(imbalance), ' -W ', subkernelWeightsFilename, ' -t ', num2str(whetherPerformTest)];
+cmdToRunPythonScript = ['./mkl.py -K ', trainkernelfilesListFilename, ' -Y ', trainlabelsFilename, ' -C ', num2str(Cval), ' -P ', num2str(mklNorm), ' -O ', predLabelsFilename, ' -T ', testkernelfilesListFilename, ' -L ', testlabelsFilename, ' -I ', num2str(imbalance), ' -W ', subkernelWeightsFilename, ' -t ', num2str(whetherPerformTest)];
 
 logMessages(debugMsgLocation, sprintf('%s', cmdToRunPythonScript), debugLevel);
 if debugLevel == 0

diff --git a/run_CoMIK.sh b/run_CoMIK.sh
@@ -18,6 +18,8 @@ else
   LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/bin/glnxa64 ;
   LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/os/glnxa64;
   LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${MCRROOT}/sys/opengl/lib/glnxa64;
+  # Uncomment the next line and append your paths here
+  # LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:<you_paths_here> ;
   export LD_LIBRARY_PATH;
   echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
   shift 1