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Recompilation for Linux/GenePattern deployment #2

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c0e8570
recompile on linux for genepattern
alex-wenzel Jun 16, 2021
7af3d02
Merge remote-tracking branch 'upstream/master'
alex-wenzel Jun 17, 2021
0f8c59d
recompile to fix cho model bug
alex-wenzel Jun 18, 2021
c22b3e7
Merge branch 'LewisLabUCSD:master' into master
alex-wenzel Jul 23, 2021
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120 changes: 42 additions & 78 deletions matlab_compiled/execCellfie.prj
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<deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
<configuration build-checksum="1860633994" file="/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie.prj" location="/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled" name="execCellfie" preferred-package-location="/media/ben/9c17f1c9-a45e-49ec-b547-8fbd2f25ccc6/CellFie/matlab_compiled/execCellfie/for_redistribution" target="target.ezdeploy.standalone" target-name="Application Compiler">
<configuration file="/home/alex/Documents/CellFie/matlab_compiled/execCellfie.prj" location="/home/alex/Documents/CellFie/matlab_compiled" name="execCellfie" target="target.ezdeploy.standalone" target-name="Application Compiler">
<param.appname>execCellfie</param.appname>
<param.icon />
<param.icons />
<param.version>0.7</param.version>
<param.authnamewatermark>Richelle, Kellman</param.authnamewatermark>
<param.email>bkellman@eng.ucsd.edu</param.email>
<param.version>1.0</param.version>
<param.authnamewatermark />
<param.email />
<param.company />
<param.summary>An alternative approach to capture the breadth of cellular functions by performing a functional analysis of existing biological networks.</param.summary>
<param.description>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 &amp; 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</param.description>
<param.summary />
<param.description />
<param.screenshot />
<param.guid />
<param.installpath.string>/execCellfie/</param.installpath.string>
<param.installpath.combo>option.installpath.systemwideapp</param.installpath.combo>
<param.installpath.combo>option.installpath.user</param.installpath.combo>
<param.logo />
<param.install.notes />
<param.target.install.notes>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.
<param.target.install.notes>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</param.target.install.notes>
${LD_LIBRARY_PATH}:MR/v94/runtime/glnxa64:MR/v94/bin/glnxa64:MR/v94/sys/os/glnxa64:MR/v94/sys/opengl/lib/glnxa64</param.target.install.notes>
<param.intermediate>${PROJECT_ROOT}/execCellfie/for_testing</param.intermediate>
<param.files.only>${PROJECT_ROOT}/execCellfie/for_redistribution_files_only</param.files.only>
<param.output>${PROJECT_ROOT}/execCellfie/for_redistribution</param.output>
Expand All @@ -62,7 +53,12 @@ ${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci6
<unset>
<param.icon />
<param.icons />
<param.version />
<param.authnamewatermark />
<param.email />
<param.company />
<param.summary />
<param.description />
<param.screenshot />
<param.guid />
<param.installpath.string />
Expand Down Expand Up @@ -92,77 +88,45 @@ ${DYLD_LIBRARY_PATH}:MR/v95/runtime/maci64:MR/v95/sys/os/maci64:MR/v95/bin/maci6
<param.help.text />
</unset>
<fileset.main>
<file>/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/genepattern/execCellfie.m</file>
<file>/home/alex/Documents/CellFie/genepattern/execCellfie.m</file>
</fileset.main>
<fileset.resources>
<file>/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/input</file>
<file>/home/alex/Documents/CellFie/input</file>
<file>/home/alex/Documents/CellFie/src/CellFie.m</file>
<file>/home/alex/Documents/CellFie/src/findRxnIDs.m</file>
<file>/home/alex/Documents/CellFie/src/findUsedGenesLevels.m</file>
<file>/home/alex/Documents/CellFie/src/prctile.m</file>
<file>/home/alex/Documents/CellFie/src/runCellFie.m</file>
<file>/home/alex/Documents/CellFie/src/selectGeneFromGPR.m</file>
<file>/home/alex/Documents/CellFie/src/tabulate.m</file>
<file>/home/alex/Documents/CellFie/src/wide2long.m</file>
</fileset.resources>
<fileset.package />
<fileset.depfun>
<file>/Users/helenmasson/Dropbox/LewisLab/dev_CellFie/NewCellFie_May29/src/CellFie.m</file>
<file>/Users/helenmasson/Dropbox/LewisLab/dev_CellFie/NewCellFie_May29/src/prctile.m</file>
<file>/Users/helenmasson/Dropbox/LewisLab/dev_CellFie/NewCellFie_May29/src/tabulate.m</file>
<file>/Users/helenmasson/cobratoolbox/src/analysis/exploration/findRxnIDs.m</file>
<file>/Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/GPRparser.m</file>
<file>/Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/findUsedGenesLevels.m</file>
<file>/Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/mapExpressionToReactions.m</file>
<file>/Users/helenmasson/cobratoolbox/src/dataIntegration/transcriptomics/preprocessing/selectGeneFromGPR.m</file>
<file>/Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/AndNode.m</file>
<file>/Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/FormulaParser.m</file>
<file>/Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/LiteralNode.m</file>
<file>/Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/Node.m</file>
<file>/Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/OrNode.m</file>
<file>/Users/helenmasson/cobratoolbox/src/reconstruction/refinement/GPRLogic/combineChildren.m</file>
</fileset.depfun>
<fileset.depfun />
<build-deliverables>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="run_execCellfie.sh" optional="false">/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="readme.txt" optional="true">/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/readme.txt</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="splash.png" optional="false">/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/splash.png</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="execCellfie.app" optional="false">/Users/helenmasson/Desktop/SenateExam/Aim2_CellFie/Final_compiledCellFIE/CellFie/matlab_compiled/execCellfie/for_testing/execCellfie.app</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="readme.txt" optional="true">/home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/readme.txt</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="run_execCellfie.sh" optional="false">/home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/run_execCellfie.sh</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="execCellfie" optional="false">/home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/execCellfie</file>
<file location="${PROJECT_ROOT}/execCellfie/for_testing" name="splash.png" optional="false">/home/alex/Documents/CellFie/matlab_compiled/execCellfie/for_testing/splash.png</file>
</build-deliverables>
<workflow />
<matlab>
<root>/Applications/MATLAB_R2018b.app</root>
<toolboxes>
<toolbox name="matlabcoder" />
<toolbox name="fixedpoint" />
<toolbox name="matlabhdlcoder" />
<toolbox name="neuralnetwork" />
</toolboxes>
<toolbox>
<matlabcoder>
<enabled>true</enabled>
</matlabcoder>
</toolbox>
<toolbox>
<fixedpoint>
<enabled>true</enabled>
</fixedpoint>
</toolbox>
<toolbox>
<matlabhdlcoder>
<enabled>true</enabled>
</matlabhdlcoder>
</toolbox>
<toolbox>
<neuralnetwork>
<enabled>true</enabled>
</neuralnetwork>
</toolbox>
<root>/usr/local/MATLAB/R2018a</root>
<toolboxes />
</matlab>
<platform>
<unix>true</unix>
<mac>true</mac>
<mac>false</mac>
<windows>false</windows>
<win2k>false</win2k>
<winxp>false</winxp>
<vista>false</vista>
<linux>false</linux>
<linux>true</linux>
<solaris>false</solaris>
<osver>10.15.7</osver>
<osver>5.8.0-55-generic</osver>
<os32>false</os32>
<os64>true</os64>
<arch>maci64</arch>
<arch>glnxa64</arch>
<matlab>true</matlab>
</platform>
</configuration>
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19 changes: 7 additions & 12 deletions matlab_compiled/execCellfie/PackagingLog.html
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<html><meta charset="UTF-8"><pre>
<font color=blue>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 </font>
Compiler version: 7.0 (R2018b)
<font color=blue>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 </font>
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".
<font color=blue>Packaging...</font>
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.
</pre></html>
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