Support for v8.6 in addition to 9.0. For compatibility, print functio…

…n in analyze_wvector fixed. test_install script to perform test upon installation.

README.md

@@ -9,9 +9,9 @@ To appear in Proceedings of WABI 2017.
 bioRxiv DOI: https://doi.org/10.1101/139618
 
 ## Requirements:
-- MATLAB 9.0.0.341360 (R2016a) [We developed _CoMIK_ using this version of MATLAB. Compatibility with earlier versions is to be checked.]
+- MATLAB 9.0.0.341360 (R2016a) [We developed _CoMIK_ using this version of MATLAB (R2016a). Compatbility checked with version R2015b]
 - Python 2.7 or higher
-- SHOGUN Release version 3.2.0 [See issue #7 (issues/7) in this regard]
+- SHOGUN Release version 3.2.0 [See issue #7 (issues/7) in this regard. _CoMIK_ also works with the latest SHOGUN version 6.0.0]
 
 For the visualizations, the following R (R version 3.4.0) packages are needed
 - Lattice (lattice_0.20-35)
@@ -21,11 +21,22 @@ This repository contains Matlab code for the project *CoMIK*. The various ".m" f
 We use MKL implementation from Shogun's modular interface for Python. The Python script mkl.py handles solving of the MKL problem.
 
 ## Installation:
-```MATLAB
+```
 git clone https://github.molgen.mpg.de/snikumbh/comik.git
 cd comik
 sh install.sh
 ```
+Once the dependencies are handled, e.g., SHOGUN, MATLAB runtime etc., you can test the installation as follows
+
+```
+sh test_install.sh 
+```
+This performs the test for both, the executable and from inside MATLAB. For testing either of them, use
+```
+sh test_install.sh executable <your_MCR_path_here>
+OR
+sh test_install.sh matlab
+```
 
 ## Usage:
 - If you have MATLAB, see the example config file `config-comik.txt`, for an example function call from inside Matlab:
@@ -34,12 +45,17 @@ For simulated dataset 1 provided in the folder `sample_data/simulated_dataset1`
 comik_wrapper('config-comik.txt');
 ```
 
-- For those who do not have MATLAB, we provide an executable which can be run as follows:
+- For those who do not have MATLAB, we provide an executable. Additionally, you require only the MATLAB Runtime installed. The appropriate version can be downloaded from https://mathworks.com/products/compiler/mcr.html .
+- Follow the instructions for installation of the MATLAB Runtime; install at any location of your choice on the disk.
+- Once installed, provide the corresponding path when running the shell script `run_CoMIK.sh` as follows:
+
 ```
-./run_CoMIK.sh <MATLAB_Runtime_location> <config_file>
-./run_CoMIK.sh /usr/lib/matlab-9.0 config-comik.txt
+./run_CoMIK_v90.sh <MATLAB_Runtime_location> <config_file>
+./run_CoMIK_v90.sh /usr/lib/matlab-9.0 config-comik.txt #for version 9.0 (R2016a)
+OR
+./run_CoMIK_v86.sh /usr/lib/matlab-8.6 config-comik.txt #for version 8.6 (R2015b)
 ```
-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`.
+where `/usr/lib/matlab-9.0` could be replaced with the location of the MATLAB runtime on your machine. Additionally, when required, you can add your own paths to the `LD_LIBRARY_PATH` environment variable in the file `run_CoMIK_v86.sh` or `run_CoMIK_v90.sh` (for example, the path for shogun can be added here).
 
 
 _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.

analyze_wvector.m

@@ -326,7 +326,7 @@
 	%set(new_ax, 'Ydir', 'reverse');
 
 	pdf_fname = strcat(folderName, '/SeqLogos_MinMax_at_distances_rank', num2str(rankId), '_oligoLen', num2str(oligoLen));
-	print(pdf_fname,'-dpdf', '-r900', '-bestfit');
+	print(pdf_fname,'-dpdf', '-r900');
 	% to produce EPS figures, use
 	% print(pdf_fname, '-depsc');
 	pdfcrop_lines = [pdfcrop_lines; sprintf('pdfcrop %s\n', pdf_fname)];

install.sh

@@ -1,4 +1,15 @@
+#!/bin/bash
+
 #Install CoMIK
 
 chmod +x mkl.py
 export PATH=".:$PATH"
+
+#Check dependenciespython -c "import modshogun"
+
+if python -c "import modshogun";
+then
+    echo "You can now run the test_install.sh script."
+else
+    echo "You need to install SHOGUN. Once done, you can run the test_install.sh script."
+fi

run_CoMIK_v86.sh

@@ -0,0 +1,33 @@
+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MATLAB Runtime environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  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;
+  export LD_LIBRARY_PATH;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=$1
+      args="${args} \"${token}\"" 
+      shift
+  done
+  eval "\"${exe_dir}/CoMIK_v86\"" $args
+fi
+exit
+

run_CoMIK_v90.sh

@@ -0,0 +1,33 @@
+#!/bin/sh
+# script for execution of deployed applications
+#
+# Sets up the MATLAB Runtime environment for the current $ARCH and executes 
+# the specified command.
+#
+exe_name=$0
+exe_dir=`dirname "$0"`
+echo "------------------------------------------"
+if [ "x$1" = "x" ]; then
+  echo Usage:
+  echo    $0 \<deployedMCRroot\> args
+else
+  echo Setting up environment variables
+  MCRROOT="$1"
+  echo ---
+  LD_LIBRARY_PATH=.:${MCRROOT}/runtime/glnxa64 ;
+  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;
+  export LD_LIBRARY_PATH;
+  echo LD_LIBRARY_PATH is ${LD_LIBRARY_PATH};
+  shift 1
+  args=
+  while [ $# -gt 0 ]; do
+      token=$1
+      args="${args} \"${token}\"" 
+      shift
+  done
+  eval "\"${exe_dir}/CoMIK_v90\"" $args
+fi
+exit
+

test_install.sh

@@ -0,0 +1,49 @@
+#!/bin/bash
+
+
+echo 'Preparing for testing ...'
+cp config-comik.txt config-comik-test.txt
+
+sed -i 's/OUTPUT_FOLDER=comik_run_simulated_dataset1/OUTPUT_FOLDER=test_comik_run_simulated_dataset1/g' config-comik-test.txt
+
+sed -i 's/NUMBER_OF_CLUSTERS=\[2 5 7]/NUMBER_OF_CLUSTERS=\[7\]/g' config-comik-test.txt
+sed -i 's/SIGMA_VALUES=10\.\^\[1\:1\:2\]/SIGMA_VALUES=10\.\^\[1\]/g' config-comik-test.txt
+sed -i 's/COST_VALUES=10\.\^\[-3\:1\:3\]/COST_VALUES=10\.\^\[1\]/g' config-comik-test.txt
+
+sed -i 's/NUMBER_OF_INNER_FOLDS=5/NUMBER_OF_INNER_FOLDS=2/g' config-comik-test.txt
+sed -i 's/NUMBER_OF_OUTER_FOLDS=5/NUMBER_OF_OUTER_FOLDS=3/g' config-comik-test.txt
+
+
+if [ "$1" = "executable" ]
+then
+    echo "Only testing the executable ... this might take some time"
+    if [ "$3" = "v86" ];
+    then
+	if [ -f "run_CoMIK_v86.sh" ];
+	then
+            ./run_CoMIK_v86.sh $2 config-comik-test.txt
+	fi
+    elif [ "$3" = "v90" ];
+    then
+	if [ -f "run_CoMIK_v90.sh" ];
+	then
+            ./run_CoMIK_v90.sh $2 config-comik-test.txt
+	fi
+    else
+        echo 'No file to run.'
+    fi
+elif [ "$1" = "matlab" ]
+then
+    echo 'Only testing inside MATLAB ... this might take some time'
+    matlab -nodesktop -nodisplay -nosplash  -r "comik_wrapper('config-comik-test.txt'); exit;"
+else
+   echo 'Testing both executable and from inside matlab ... this might take some time'
+fi
+
+if [ -d "$test_comik_run_simulated_dataset1"]; then
+    rm -rf test_comik_run_simulated_dataset1/
+    rm config-comik-test.txt
+fi
+echo "Done."
+
+