diff --git a/matlab_compiled/execCellfie.prj b/matlab_compiled/execCellfie.prj index f8e3d12..065be0a 100644 --- a/matlab_compiled/execCellfie.prj +++ b/matlab_compiled/execCellfie.prj @@ -1,43 +1,34 @@ - + execCellfie - 0.7 - Richelle, Kellman - bkellman@eng.ucsd.edu + 1.0 + + - An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks. - CellFie: Cellular Functions InferencE - - -An alternative approach for the interpretation of omics data (e.g., differentially expressed genes) that captures the simplicity of enrichment analyses, while providing deeper mechanistic insights into how differential expression impacts specific cellular functions. This approach enables the investigation of hundreds of metabolic tasks curated from literature covering 7 major metabolic activities of a cell (energy generation, nucleotide, carbohydrate, amino acid, lipid, vitamin & cofactor and glycan metabolism) and 4 mammalian organisms (human, rat, mouse and CHO cells). This platform can be used to predict the activity of these metabolic functions from transcriptomic data to comprehensively quantify the propensity of a cell line or tissue to express a metabolic function. - -We welcome any comments, bug reports, and feature requests. Please send all feedback to arichelleres@gmail.com - -For issues with the GenePattern module, please contact atwenzel@eng.ucsd.edu - -Updates -8/04/20 - remove cobratoolbox dependency -3/26/2020 - added detailScores.csv output -4/09/2020 - fixed percentile setting in line 23-25 -4/09/2020 - added explicit "global" parameter -4/19/2020 - fixed execCellfie parameter bug + + /execCellfie/ - option.installpath.systemwideapp + option.installpath.user - In the following directions, replace MR/v95 by the directory on the target machine where MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed. + In the following directions, replace MR/v94 by the directory on the target machine where MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed. + +(1) Set the environment variable XAPPLRESDIR to this value: + +MR/v94/X11/app-defaults + -If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the following string: +(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the following: -MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci64 +MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64 If it is defined, set it to the following: -${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci64 +${LD_LIBRARY_PATH}:MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64 ${PROJECT_ROOT}/execCellfie/for_testing ${PROJECT_ROOT}/execCellfie/for_redistribution_files_only ${PROJECT_ROOT}/execCellfie/for_redistribution @@ -62,7 +53,12 @@ ${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci6 + + + + + @@ -92,77 +88,45 @@ ${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci6 - /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/genepattern/execCellfie.m + /home/alex/Documents/CellFie/genepattern/execCellfie.m - /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/input + /home/alex/Documents/CellFie/input + /home/alex/Documents/CellFie/src/CellFie.m + /home/alex/Documents/CellFie/src/findRxnIDs.m + /home/alex/Documents/CellFie/src/findUsedGenesLevels.m + /home/alex/Documents/CellFie/src/prctile.m + /home/alex/Documents/CellFie/src/runCellFie.m + /home/alex/Documents/CellFie/src/selectGeneFromGPR.m + /home/alex/Documents/CellFie/src/tabulate.m + /home/alex/Documents/CellFie/src/wide2long.m - - /Users/helenmasson/Dropbox/LewisLab/dev_CellFie/NewCellFie_May29/src/CellFie.m - /Users/helenmasson/Dropbox/LewisLab/dev_CellFie/NewCellFie_May29/src/prctile.m - /Users/helenmasson/Dropbox/LewisLab/dev_CellFie/NewCellFie_May29/src/tabulate.m - /Users/helenmasson/cobratoolbox/src/analysis/exploration/findRxnIDs.m - /Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/GPRparser.m - /Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/findUsedGenesLevels.m - /Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/mapExpressionToReactions.m - /Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/selectGeneFromGPR.m - /Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/AndNode.m - /Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/FormulaParser.m - /Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/LiteralNode.m - /Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/Node.m - /Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/OrNode.m - /Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/combineChildren.m - + - /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh - /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/readme.txt - /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/splash.png - /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/execCellfie.app + /home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/readme.txt + /home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh + /home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/execCellfie + /home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/splash.png - /Applications/MATLAB_R2018b.app - - - - - - - - - true - - - - - true - - - - - true - - - - - true - - + /usr/local/MATLAB/R2018a + true - true + false false false false false - false + true false - 10.15.7 + 5.8.0-55-generic false true - maci64 + glnxa64 true diff --git a/matlab_compiled/execCellfie/PackagingLog.html b/matlab_compiled/execCellfie/PackagingLog.html index b6edfe6..bf598cb 100644 --- a/matlab_compiled/execCellfie/PackagingLog.html +++ b/matlab_compiled/execCellfie/PackagingLog.html @@ -1,22 +1,17 @@ 
-mcc -o execCellfie -W main:execCellfie -T link:exe -d /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing -v /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/genepattern/execCellfie.m -a /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/input 
-Compiler version: 7.0 (R2018b)
+mcc -o execCellfie -W main:execCellfie -T link:exe -d /home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing -v /home/alex/Documents/CellFie/genepattern/execCellfie.m -a /home/alex/Documents/CellFie/src/CellFie.m -a /home/alex/Documents/CellFie/src/findRxnIDs.m -a /home/alex/Documents/CellFie/src/findUsedGenesLevels.m -a /home/alex/Documents/CellFie/input -a /home/alex/Documents/CellFie/src/prctile.m -a /home/alex/Documents/CellFie/src/runCellFie.m -a /home/alex/Documents/CellFie/src/selectGeneFromGPR.m -a /home/alex/Documents/CellFie/src/tabulate.m -a /home/alex/Documents/CellFie/src/wide2long.m 
+Compiler version: 6.6 (R2018a)
 
 Dependency analysis by REQUIREMENTS.
 
-Parsing file "/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/genepattern/execCellfie.m"
+Parsing file "/home/alex/Documents/CellFie/genepattern/execCellfie.m"
 	(Referenced from: "Compiler Command Line").
 Deleting 0 temporary MEX authorization files.
-Generating file "/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/readme.txt".
-Generating file "/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh".
+Generating file "/home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/readme.txt".
+Generating file "/home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh".
 Packaging...
-Adding custom icon /Applications/MATLAB_R2018b.app/toolbox/compiler/Resources/default_icon.icns to /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/execCellfie.app.
 Creating the bundle...
-Copying /Applications/MATLAB_R2018b.app/toolbox/compiler/maci64/setup.app to /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app.
-Copying /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_redistribution/bundle.zip to /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/bundle.zip.
-Copying /Applications/MATLAB_R2018b.app/toolbox/compiler/Resources/default_splash.png to /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/splash.png.
-Copying /Applications/MATLAB_R2018b.app/toolbox/compiler/Resources/default_icon.icns to /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/installer.icns.
-Web based installer created at /Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app.
+Web based installer created at /home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.install.
 Packaging complete.
-Elapsed packaging time was: 1 minutes and 4 seconds.
+Elapsed packaging time was: 1 minutes and 23 seconds.
diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Info.plist b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Info.plist deleted file mode 100644 index db9c7f7..0000000 --- a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Info.plist +++ /dev/null @@ -1,43 +0,0 @@ - - - - - CFBundleDevelopmentRegion - en - CFBundleExecutable - setup - CFBundleIconFile - installer.icns - CFBundleIdentifier - com.mathworks.toolbox.compiler.setup - CFBundleInfoDictionaryVersion - 6.0 - CFBundlePackageType - APPL - CFBundleShortVersionString - 1.0 - CFBundleSignature - ???? - CFBundleVersion - 1 - LSMinimumSystemVersion - 10.4 - NSMainNibFile - MainMenu - NSPrincipalClass - NSApplication - NSAppTransportSecurity - - NSExceptionDomains - - mathworks.com - - NSIncludesSubdomains - - NSThirdPartyExceptionRequiresForwardSecrecy - - - - - - diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup deleted file mode 100755 index 7c34890..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup.dSYM/Contents/Info.plist b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup.dSYM/Contents/Info.plist deleted file mode 100644 index 29859ca..0000000 --- a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup.dSYM/Contents/Info.plist +++ /dev/null @@ -1,20 +0,0 @@ - - - - - CFBundleDevelopmentRegion - English - CFBundleIdentifier - com.apple.xcode.dsym.com.mathworks.toolbox.compiler.setup - CFBundleInfoDictionaryVersion - 6.0 - CFBundlePackageType - dSYM - CFBundleSignature - ???? - CFBundleShortVersionString - 1.0 - CFBundleVersion - 1 - - diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup.dSYM/Contents/Resources/DWARF/setup b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup.dSYM/Contents/Resources/DWARF/setup deleted file mode 100644 index d8aa28f..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/MacOS/setup.dSYM/Contents/Resources/DWARF/setup and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/bundle.zip b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/bundle.zip deleted file mode 100644 index ddb40e1..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/bundle.zip and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/en.lproj/MainMenu.nib b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/en.lproj/MainMenu.nib deleted file mode 100644 index fd50315..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/en.lproj/MainMenu.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/installer.icns b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/installer.icns deleted file mode 100755 index 8f10702..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/installer.icns and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/splash.png b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/splash.png deleted file mode 100644 index d60c6fa..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.app/Contents/Resources/splash.png and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.install b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.install index 38c2c1f..904824b 100755 Binary files a/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.install and b/matlab_compiled/execCellfie/for_redistribution/MyAppInstaller_web.install differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/default_icon.icns b/matlab_compiled/execCellfie/for_redistribution_files_only/default_icon.icns deleted file mode 100755 index 8f10702..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/default_icon.icns and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie index 7f71f7c..bb4beef 100755 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie and b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Info.plist b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Info.plist deleted file mode 100644 index a4072e2..0000000 --- a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Info.plist +++ /dev/null @@ -1,34 +0,0 @@ - - - - - CFBundleDevelopmentRegion - English - CFBundleExecutable - prelaunch - CFBundleIconFile - membrane.icns - CFBundleIdentifier - execCellfie - CFBundleInfoDictionaryVersion - 6.0 - CFBundleName - execCellfie - CFBundlePackageType - APPL - CFBundleSignature - execCellfie - CFBundleVersion - 1 - CFBundleVersionString - 1.0 - CFResourcesFileMapped - - LSMinimumSystemVersion - 10.9.0 - NSMainNibFile - MainMenu - NSPrincipalClass - NSApplication - - diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/applauncher b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/applauncher deleted file mode 100755 index a682c0d..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/applauncher and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/execCellfie b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/execCellfie deleted file mode 100755 index 2822836..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/execCellfie and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/prelaunch b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/prelaunch deleted file mode 100755 index 8a92bdc..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/MacOS/prelaunch and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/About.nib b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/About.nib deleted file mode 100644 index fe0958e..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/About.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MWOpenAccessoryView.nib b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MWOpenAccessoryView.nib deleted file mode 100644 index dda21bf..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MWOpenAccessoryView.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MWSaveAccessoryView.nib b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MWSaveAccessoryView.nib deleted file mode 100644 index 690b8ed..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MWSaveAccessoryView.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MainMenu.nib b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MainMenu.nib deleted file mode 100644 index 3095496..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/Base.lproj/MainMenu.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/membrane.icns b/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/membrane.icns deleted file mode 100755 index 8f10702..0000000 Binary files a/matlab_compiled/execCellfie/for_redistribution_files_only/execCellfie.app/Contents/Resources/membrane.icns and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/readme.txt b/matlab_compiled/execCellfie/for_redistribution_files_only/readme.txt index 9fe8cb1..3edd0de 100644 --- a/matlab_compiled/execCellfie/for_redistribution_files_only/readme.txt +++ b/matlab_compiled/execCellfie/for_redistribution_files_only/readme.txt @@ -2,58 +2,53 @@ execCellfie Executable 1. Prerequisites for Deployment -Verify that version 9.5 (R2018b) of the MATLAB Runtime is installed. +Verify that version 9.4 (R2018a) of the MATLAB Runtime is installed. If not, you can run the MATLAB Runtime installer. To find its location, enter >>mcrinstaller at the MATLAB prompt. -NOTE: You will need administrator rights to run the MATLAB Runtime installer. -Alternatively, download and install the Macintosh version of the MATLAB Runtime for R2018b +Alternatively, download and install the Linux version of the MATLAB Runtime for R2018a from the following link on the MathWorks website: http://www.mathworks.com/products/compiler/mcr/index.html For more information about the MATLAB Runtime and the MATLAB Runtime installer, see -"Distribute Applications" in the MATLAB Compiler documentation +Package and Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center. 2. Files to Deploy and Package Files to Package for Standalone ================================ +-execCellfie -run_execCellfie.sh (shell script for temporarily setting environment variables and - executing the application) + executing the application) -to run the shell script, type ./run_execCellfie.sh at Linux or Mac command prompt. is the directory - where version 9.5 of the MATLAB Runtime is installed or the directory where + where version 9.4 of the MATLAB Runtime is installed or the directory where MATLAB is installed on the machine. is all the arguments you want to pass to your application. For example, - If you have version 9.5 of the MATLAB Runtime installed in - /mathworks/home/application/v95, run the shell script as: + If you have version 9.4 of the MATLAB Runtime installed in + /mathworks/home/application/v94, run the shell script as: - ./run_execCellfie.sh /mathworks/home/application/v95 + ./run_execCellfie.sh /mathworks/home/application/v94 If you have MATLAB installed in /mathworks/devel/application/matlab, run the shell script as: ./run_execCellfie.sh /mathworks/devel/application/matlab --MCRInstaller.zip +-MCRInstaller.zip Note: if end users are unable to download the MATLAB Runtime using the instructions in the previous section, include it when building your component by clicking the "Runtime included in package" link in the Deployment Tool. --The Macintosh bundle directory structure execCellfie.app - Note: this can be stored in an archive file with the zip command - zip -r execCellfie.zip execCellfie.app - or the tar command - tar -cvf execCellfie.tar execCellfie.app -This readme file @@ -68,18 +63,22 @@ Center. 4. Appendix -A. Mac systems: -In the following directions, replace MR/v95 by the directory on the target machine where +A. Linux systems: +In the following directions, replace MR/v94 by the directory on the target machine where MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed. -If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the following - string: +(1) Set the environment variable XAPPLRESDIR to this value: -MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci64 +MR/v94/X11/app-defaults + + +(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the following: + +MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64 If it is defined, set it to the following: -${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci64 +${LD_LIBRARY_PATH}:MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64 For more detailed information about setting the MATLAB Runtime paths, see Package and Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center. @@ -98,11 +97,6 @@ ${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci6 -5. Launching application using Macintosh finder - -If the application is purely graphical, that is, it doesn't read from standard in or -write to standard out or standard error, it may be launched in the finder just like any -other Macintosh application. diff --git a/matlab_compiled/execCellfie/for_redistribution_files_only/run_execCellfie.sh b/matlab_compiled/execCellfie/for_redistribution_files_only/run_execCellfie.sh index a780290..5f3124c 100755 --- a/matlab_compiled/execCellfie/for_redistribution_files_only/run_execCellfie.sh +++ b/matlab_compiled/execCellfie/for_redistribution_files_only/run_execCellfie.sh @@ -14,11 +14,12 @@ else echo Setting up environment variables MCRROOT="$1" echo --- - DYLD_LIBRARY_PATH=.:${MCRROOT}/runtime/maci64 ; - DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${MCRROOT}/bin/maci64 ; - DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${MCRROOT}/sys/os/maci64; - export DYLD_LIBRARY_PATH; - echo DYLD_LIBRARY_PATH is ${DYLD_LIBRARY_PATH}; + LD_LIBRARY_PATH=.:${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 [ $# -gt 0 ]; do @@ -26,7 +27,7 @@ else args="${args} \"${token}\"" shift done - eval "\"${exe_dir}/execCellfie.app/Contents/MacOS/execCellfie\"" $args + eval "\"${exe_dir}/execCellfie\"" $args fi exit diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie b/matlab_compiled/execCellfie/for_testing/execCellfie index 7f71f7c..bb4beef 100755 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie and b/matlab_compiled/execCellfie/for_testing/execCellfie differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Info.plist b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Info.plist deleted file mode 100644 index a4072e2..0000000 --- a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Info.plist +++ /dev/null @@ -1,34 +0,0 @@ - - - - - CFBundleDevelopmentRegion - English - CFBundleExecutable - prelaunch - CFBundleIconFile - membrane.icns - CFBundleIdentifier - execCellfie - CFBundleInfoDictionaryVersion - 6.0 - CFBundleName - execCellfie - CFBundlePackageType - APPL - CFBundleSignature - execCellfie - CFBundleVersion - 1 - CFBundleVersionString - 1.0 - CFResourcesFileMapped - - LSMinimumSystemVersion - 10.9.0 - NSMainNibFile - MainMenu - NSPrincipalClass - NSApplication - - diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/applauncher b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/applauncher deleted file mode 100755 index a682c0d..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/applauncher and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/execCellfie b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/execCellfie deleted file mode 100755 index 2822836..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/execCellfie and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/prelaunch b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/prelaunch deleted file mode 100755 index 8a92bdc..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/MacOS/prelaunch and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/About.nib b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/About.nib deleted file mode 100644 index fe0958e..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/About.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MWOpenAccessoryView.nib b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MWOpenAccessoryView.nib deleted file mode 100644 index dda21bf..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MWOpenAccessoryView.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MWSaveAccessoryView.nib b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MWSaveAccessoryView.nib deleted file mode 100644 index 690b8ed..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MWSaveAccessoryView.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MainMenu.nib b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MainMenu.nib deleted file mode 100644 index 3095496..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/Base.lproj/MainMenu.nib and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/membrane.icns b/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/membrane.icns deleted file mode 100755 index 8f10702..0000000 Binary files a/matlab_compiled/execCellfie/for_testing/execCellfie.app/Contents/Resources/membrane.icns and /dev/null differ diff --git a/matlab_compiled/execCellfie/for_testing/readme.txt b/matlab_compiled/execCellfie/for_testing/readme.txt index 9fe8cb1..3edd0de 100644 --- a/matlab_compiled/execCellfie/for_testing/readme.txt +++ b/matlab_compiled/execCellfie/for_testing/readme.txt @@ -2,58 +2,53 @@ execCellfie Executable 1. Prerequisites for Deployment -Verify that version 9.5 (R2018b) of the MATLAB Runtime is installed. +Verify that version 9.4 (R2018a) of the MATLAB Runtime is installed. If not, you can run the MATLAB Runtime installer. To find its location, enter >>mcrinstaller at the MATLAB prompt. -NOTE: You will need administrator rights to run the MATLAB Runtime installer. -Alternatively, download and install the Macintosh version of the MATLAB Runtime for R2018b +Alternatively, download and install the Linux version of the MATLAB Runtime for R2018a from the following link on the MathWorks website: http://www.mathworks.com/products/compiler/mcr/index.html For more information about the MATLAB Runtime and the MATLAB Runtime installer, see -"Distribute Applications" in the MATLAB Compiler documentation +Package and Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center. 2. Files to Deploy and Package Files to Package for Standalone ================================ +-execCellfie -run_execCellfie.sh (shell script for temporarily setting environment variables and - executing the application) + executing the application) -to run the shell script, type ./run_execCellfie.sh at Linux or Mac command prompt. is the directory - where version 9.5 of the MATLAB Runtime is installed or the directory where + where version 9.4 of the MATLAB Runtime is installed or the directory where MATLAB is installed on the machine. is all the arguments you want to pass to your application. For example, - If you have version 9.5 of the MATLAB Runtime installed in - /mathworks/home/application/v95, run the shell script as: + If you have version 9.4 of the MATLAB Runtime installed in + /mathworks/home/application/v94, run the shell script as: - ./run_execCellfie.sh /mathworks/home/application/v95 + ./run_execCellfie.sh /mathworks/home/application/v94 If you have MATLAB installed in /mathworks/devel/application/matlab, run the shell script as: ./run_execCellfie.sh /mathworks/devel/application/matlab --MCRInstaller.zip +-MCRInstaller.zip Note: if end users are unable to download the MATLAB Runtime using the instructions in the previous section, include it when building your component by clicking the "Runtime included in package" link in the Deployment Tool. --The Macintosh bundle directory structure execCellfie.app - Note: this can be stored in an archive file with the zip command - zip -r execCellfie.zip execCellfie.app - or the tar command - tar -cvf execCellfie.tar execCellfie.app -This readme file @@ -68,18 +63,22 @@ Center. 4. Appendix -A. Mac systems: -In the following directions, replace MR/v95 by the directory on the target machine where +A. Linux systems: +In the following directions, replace MR/v94 by the directory on the target machine where MATLAB is installed, or MR by the directory where the MATLAB Runtime is installed. -If the environment variable DYLD_LIBRARY_PATH is undefined, set it to the following - string: +(1) Set the environment variable XAPPLRESDIR to this value: -MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci64 +MR/v94/X11/app-defaults + + +(2) If the environment variable LD_LIBRARY_PATH is undefined, set it to the following: + +MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64 If it is defined, set it to the following: -${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci64 +${LD_LIBRARY_PATH}:MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64 For more detailed information about setting the MATLAB Runtime paths, see Package and Distribute in the MATLAB Compiler documentation in the MathWorks Documentation Center. @@ -98,11 +97,6 @@ ${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci6 -5. Launching application using Macintosh finder - -If the application is purely graphical, that is, it doesn't read from standard in or -write to standard out or standard error, it may be launched in the finder just like any -other Macintosh application. diff --git a/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh b/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh index a780290..5f3124c 100755 --- a/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh +++ b/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh @@ -14,11 +14,12 @@ else echo Setting up environment variables MCRROOT="$1" echo --- - DYLD_LIBRARY_PATH=.:${MCRROOT}/runtime/maci64 ; - DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${MCRROOT}/bin/maci64 ; - DYLD_LIBRARY_PATH=${DYLD_LIBRARY_PATH}:${MCRROOT}/sys/os/maci64; - export DYLD_LIBRARY_PATH; - echo DYLD_LIBRARY_PATH is ${DYLD_LIBRARY_PATH}; + LD_LIBRARY_PATH=.:${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 [ $# -gt 0 ]; do @@ -26,7 +27,7 @@ else args="${args} \"${token}\"" shift done - eval "\"${exe_dir}/execCellfie.app/Contents/MacOS/execCellfie\"" $args + eval "\"${exe_dir}/execCellfie\"" $args fi exit