From f48f172095018a1829d6de7a2b77e0d49eeed04a Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Wed, 22 May 2024 10:55:06 +0200 Subject: [PATCH] fix: checkInstallation new libSBML filenames --- doc/installation/checkInstallation.html | 78 +++++++++++++------------ installation/checkInstallation.m | 22 +++---- 2 files changed, 52 insertions(+), 48 deletions(-) diff --git a/doc/installation/checkInstallation.html b/doc/installation/checkInstallation.html index 58b3c801..02a58994 100644 --- a/doc/installation/checkInstallation.html +++ b/doc/installation/checkInstallation.html @@ -188,7 +188,7 @@

SOURCE CODE ^try 0127 evalc('importModel(fullfile(ravenDir,''tutorial'',''empty.xml''))'); 0128 try -0129 libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+ +0129 libSBMLver=OutputSBML_RAVEN; % Only works in libSBML 5.17.0+ 0130 fprintf([libSBMLver.libSBML_version_string '\n']); 0131 catch 0132 printOrange('Fail\n') @@ -375,43 +375,45 @@

SOURCE CODE ^end 0314 0315 function status = makeBinaryExecutable(ravenDir) -0316 if ispc -0317 status = 0; % No need to run on Windows -0318 return; -0319 end -0320 binDir = fullfile(ravenDir,'software'); -0321 -0322 binList = {fullfile(binDir,'blast+','blastp'); fullfile(binDir,'blast+','blastp.mac'); -0323 fullfile(binDir,'blast+','makeblastdb'); fullfile(binDir,'blast+','makeblastdb.mac'); -0324 fullfile(binDir,'cd-hit','cd-hit'); fullfile(binDir,'cd-hit','cd-hit.mac'); -0325 fullfile(binDir,'diamond','diamond'); fullfile(binDir,'diamond','diamond.mac'); -0326 fullfile(binDir,'hmmer','hmmbuild'); fullfile(binDir,'hmmer','hmmbuild.mac'); -0327 fullfile(binDir,'hmmer','hmmsearch'); fullfile(binDir,'hmmer','hmmsearch.mac'); -0328 fullfile(binDir,'GLPKmex','glpkcc.mexa64'); fullfile(binDir,'GLPKmex','glpkcc.mexglx'); fullfile(binDir,'GLPKmex','glpkcc.mexmaci64'); -0329 fullfile(binDir,'libSBML','TranslateSBML.mexa64'); fullfile(binDir,'libSBML','TranslateSBML.mexglx'); fullfile(binDir,'libSBML','TranslateSBML.mexmaci64'); -0330 fullfile(binDir,'libSBML','OutputSBML.mexa64'); fullfile(binDir,'libSBML','OutputSBML.mexglx'); fullfile(binDir,'libSBML','OutputSBML.mexmaci64'); -0331 fullfile(binDir,'mafft','mafft-linux64','mafft.bat'); -0332 fullfile(binDir,'mafft','mafft-mac','mafft.bat');}; -0333 -0334 for i=1:numel(binList) -0335 [status,cmdout] = system(['chmod +x "' binList{i} '"']); -0336 if status ~= 0 -0337 warning('Failed to make %s executable: %s ',binList{i},strip(cmdout)) -0338 end -0339 end -0340 end -0341 -0342 function printOrange(stringToPrint) -0343 % printOrange -0344 % Duplicate of RAVEN/core/printOrange is also kept here, as this function -0345 % should be able to run before adding RAVEN to the MATLAB path. -0346 try useDesktop = usejava('desktop'); catch, useDesktop = false; end -0347 if useDesktop -0348 fprintf(['[\b' stringToPrint,']\b']) -0349 else -0350 fprintf(stringToPrint) -0351 end -0352 end +0316 % This function is required to run when RAVEN is downloaded as MATLAB +0317 % Add-On, in which case the file permissions are not correctly set +0318 if ispc +0319 status = 0; % No need to run on Windows +0320 return; +0321 end +0322 binDir = fullfile(ravenDir,'software'); +0323 +0324 binList = {fullfile(binDir,'blast+','blastp'); fullfile(binDir,'blast+','blastp.mac'); +0325 fullfile(binDir,'blast+','makeblastdb'); fullfile(binDir,'blast+','makeblastdb.mac'); +0326 fullfile(binDir,'cd-hit','cd-hit'); fullfile(binDir,'cd-hit','cd-hit.mac'); +0327 fullfile(binDir,'diamond','diamond'); fullfile(binDir,'diamond','diamond.mac'); +0328 fullfile(binDir,'hmmer','hmmbuild'); fullfile(binDir,'hmmer','hmmbuild.mac'); +0329 fullfile(binDir,'hmmer','hmmsearch'); fullfile(binDir,'hmmer','hmmsearch.mac'); +0330 fullfile(binDir,'GLPKmex','glpkcc.mexa64'); fullfile(binDir,'GLPKmex','glpkcc.mexglx'); fullfile(binDir,'GLPKmex','glpkcc.mexmaci64'); fullfile(binDir,'GLPKmex','glpkcc.mexmaca64'); +0331 fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexglx'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaci64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaca64'); +0332 fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexglx'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaci64'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaca64'); +0333 fullfile(binDir,'mafft','mafft-linux64','mafft.bat'); +0334 fullfile(binDir,'mafft','mafft-mac','mafft.bat');}; +0335 +0336 for i=1:numel(binList) +0337 [status,cmdout] = system(['chmod +x "' binList{i} '"']); +0338 if status ~= 0 +0339 warning('Failed to make %s executable: %s ',binList{i},strip(cmdout)) +0340 end +0341 end +0342 end +0343 +0344 function printOrange(stringToPrint) +0345 % printOrange +0346 % Duplicate of RAVEN/core/printOrange is also kept here, as this function +0347 % should be able to run before adding RAVEN to the MATLAB path. +0348 try useDesktop = usejava('desktop'); catch, useDesktop = false; end +0349 if useDesktop +0350 fprintf(['[\b' stringToPrint,']\b']) +0351 else +0352 fprintf(stringToPrint) +0353 end +0354 end
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\ No newline at end of file diff --git a/installation/checkInstallation.m b/installation/checkInstallation.m index 3c820dc9..5f892e3b 100755 --- a/installation/checkInstallation.m +++ b/installation/checkInstallation.m @@ -126,7 +126,7 @@ try evalc('importModel(fullfile(ravenDir,''tutorial'',''empty.xml''))'); try - libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+ + libSBMLver=OutputSBML_RAVEN; % Only works in libSBML 5.17.0+ fprintf([libSBMLver.libSBML_version_string '\n']); catch printOrange('Fail\n') @@ -313,21 +313,23 @@ end function status = makeBinaryExecutable(ravenDir) +% This function is required to run when RAVEN is downloaded as MATLAB +% Add-On, in which case the file permissions are not correctly set if ispc status = 0; % No need to run on Windows return; end binDir = fullfile(ravenDir,'software'); -binList = {fullfile(binDir,'blast+','blastp'); fullfile(binDir,'blast+','blastp.mac'); - fullfile(binDir,'blast+','makeblastdb'); fullfile(binDir,'blast+','makeblastdb.mac'); - fullfile(binDir,'cd-hit','cd-hit'); fullfile(binDir,'cd-hit','cd-hit.mac'); - fullfile(binDir,'diamond','diamond'); fullfile(binDir,'diamond','diamond.mac'); - fullfile(binDir,'hmmer','hmmbuild'); fullfile(binDir,'hmmer','hmmbuild.mac'); - fullfile(binDir,'hmmer','hmmsearch'); fullfile(binDir,'hmmer','hmmsearch.mac'); - fullfile(binDir,'GLPKmex','glpkcc.mexa64'); fullfile(binDir,'GLPKmex','glpkcc.mexglx'); fullfile(binDir,'GLPKmex','glpkcc.mexmaci64'); - fullfile(binDir,'libSBML','TranslateSBML.mexa64'); fullfile(binDir,'libSBML','TranslateSBML.mexglx'); fullfile(binDir,'libSBML','TranslateSBML.mexmaci64'); - fullfile(binDir,'libSBML','OutputSBML.mexa64'); fullfile(binDir,'libSBML','OutputSBML.mexglx'); fullfile(binDir,'libSBML','OutputSBML.mexmaci64'); +binList = {fullfile(binDir,'blast+','blastp'); fullfile(binDir,'blast+','blastp.mac'); + fullfile(binDir,'blast+','makeblastdb'); fullfile(binDir,'blast+','makeblastdb.mac'); + fullfile(binDir,'cd-hit','cd-hit'); fullfile(binDir,'cd-hit','cd-hit.mac'); + fullfile(binDir,'diamond','diamond'); fullfile(binDir,'diamond','diamond.mac'); + fullfile(binDir,'hmmer','hmmbuild'); fullfile(binDir,'hmmer','hmmbuild.mac'); + fullfile(binDir,'hmmer','hmmsearch'); fullfile(binDir,'hmmer','hmmsearch.mac'); + fullfile(binDir,'GLPKmex','glpkcc.mexa64'); fullfile(binDir,'GLPKmex','glpkcc.mexglx'); fullfile(binDir,'GLPKmex','glpkcc.mexmaci64'); fullfile(binDir,'GLPKmex','glpkcc.mexmaca64'); + fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexglx'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaci64'); fullfile(binDir,'libSBML','TranslateSBML_RAVEN.mexmaca64'); + fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexa64'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexglx'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaci64'); fullfile(binDir,'libSBML','OutputSBML_RAVEN.mexmaca64'); fullfile(binDir,'mafft','mafft-linux64','mafft.bat'); fullfile(binDir,'mafft','mafft-mac','mafft.bat');};