Skip to content

Commit

Permalink
fix: checkInstallation new libSBML filenames
Browse files Browse the repository at this point in the history
  • Loading branch information
@edkerk
edkerk committed May 22, 2024
1 parent a2abfa9 commit 493ce8d
Show file tree
Hide file tree
Showing 2 changed files with 52 additions and 48 deletions.
78 changes: 40 additions & 38 deletions doc/installation/checkInstallation.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -188,7 +188,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0126 <span class="keyword">try</span>
0127 evalc(<span class="string">'importModel(fullfile(ravenDir,''tutorial'',''empty.xml''))'</span>);
0128 <span class="keyword">try</span>
0129 libSBMLver=OutputSBML; <span class="comment">% Only works in libSBML 5.17.0+</span>
0129 libSBMLver=OutputSBML_RAVEN; <span class="comment">% Only works in libSBML 5.17.0+</span>
0130 fprintf([libSBMLver.libSBML_version_string <span class="string">'\n'</span>]);
0131 <span class="keyword">catch</span>
0132 <a href="#_sub4" class="code" title="subfunction printOrange(stringToPrint)">printOrange</a>(<span class="string">'Fail\n'</span>)
Expand Down Expand Up @@ -375,43 +375,45 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0313 <span class="keyword">end</span>
0314
0315 <a name="_sub3" href="#_subfunctions" class="code">function status = makeBinaryExecutable(ravenDir)</a>
0316 <span class="keyword">if</span> ispc
0317 status = 0; <span class="comment">% No need to run on Windows</span>
0318 <span class="keyword">return</span>;
0319 <span class="keyword">end</span>
0320 binDir = fullfile(ravenDir,<span class="string">'software'</span>);
0321
0322 binList = {fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'blastp'</span>); fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'blastp.mac'</span>);
0323 fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'makeblastdb'</span>); fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'makeblastdb.mac'</span>);
0324 fullfile(binDir,<span class="string">'cd-hit'</span>,<span class="string">'cd-hit'</span>); fullfile(binDir,<span class="string">'cd-hit'</span>,<span class="string">'cd-hit.mac'</span>);
0325 fullfile(binDir,<span class="string">'diamond'</span>,<span class="string">'diamond'</span>); fullfile(binDir,<span class="string">'diamond'</span>,<span class="string">'diamond.mac'</span>);
0326 fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmbuild'</span>); fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmbuild.mac'</span>);
0327 fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmsearch'</span>); fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmsearch.mac'</span>);
0328 fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexa64'</span>); fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexglx'</span>); fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexmaci64'</span>);
0329 fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML.mexa64'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML.mexglx'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML.mexmaci64'</span>);
0330 fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML.mexa64'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML.mexglx'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML.mexmaci64'</span>);
0331 fullfile(binDir,<span class="string">'mafft'</span>,<span class="string">'mafft-linux64'</span>,<span class="string">'mafft.bat'</span>);
0332 fullfile(binDir,<span class="string">'mafft'</span>,<span class="string">'mafft-mac'</span>,<span class="string">'mafft.bat'</span>);};
0333
0334 <span class="keyword">for</span> i=1:numel(binList)
0335 [status,cmdout] = system([<span class="string">'chmod +x &quot;'</span> binList{i} <span class="string">'&quot;'</span>]);
0336 <span class="keyword">if</span> status ~= 0
0337 warning(<span class="string">'Failed to make %s executable: %s '</span>,binList{i},strip(cmdout))
0338 <span class="keyword">end</span>
0339 <span class="keyword">end</span>
0340 <span class="keyword">end</span>
0341
0342 <a name="_sub4" href="#_subfunctions" class="code">function printOrange(stringToPrint)</a>
0343 <span class="comment">% printOrange</span>
0344 <span class="comment">% Duplicate of RAVEN/core/printOrange is also kept here, as this function</span>
0345 <span class="comment">% should be able to run before adding RAVEN to the MATLAB path.</span>
0346 <span class="keyword">try</span> useDesktop = usejava(<span class="string">'desktop'</span>); <span class="keyword">catch</span>, useDesktop = false; <span class="keyword">end</span>
0347 <span class="keyword">if</span> useDesktop
0348 fprintf([<span class="string">'[\b'</span> stringToPrint,<span class="string">']\b'</span>])
0349 <span class="keyword">else</span>
0350 fprintf(stringToPrint)
0351 <span class="keyword">end</span>
0352 <span class="keyword">end</span></pre></div>
0316 <span class="comment">% This function is required to run when RAVEN is downloaded as MATLAB</span>
0317 <span class="comment">% Add-On, in which case the file permissions are not correctly set</span>
0318 <span class="keyword">if</span> ispc
0319 status = 0; <span class="comment">% No need to run on Windows</span>
0320 <span class="keyword">return</span>;
0321 <span class="keyword">end</span>
0322 binDir = fullfile(ravenDir,<span class="string">'software'</span>);
0323
0324 binList = {fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'blastp'</span>); fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'blastp.mac'</span>);
0325 fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'makeblastdb'</span>); fullfile(binDir,<span class="string">'blast+'</span>,<span class="string">'makeblastdb.mac'</span>);
0326 fullfile(binDir,<span class="string">'cd-hit'</span>,<span class="string">'cd-hit'</span>); fullfile(binDir,<span class="string">'cd-hit'</span>,<span class="string">'cd-hit.mac'</span>);
0327 fullfile(binDir,<span class="string">'diamond'</span>,<span class="string">'diamond'</span>); fullfile(binDir,<span class="string">'diamond'</span>,<span class="string">'diamond.mac'</span>);
0328 fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmbuild'</span>); fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmbuild.mac'</span>);
0329 fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmsearch'</span>); fullfile(binDir,<span class="string">'hmmer'</span>,<span class="string">'hmmsearch.mac'</span>);
0330 fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexa64'</span>); fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexglx'</span>); fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexmaci64'</span>); fullfile(binDir,<span class="string">'GLPKmex'</span>,<span class="string">'glpkcc.mexmaca64'</span>);
0331 fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML_RAVEN.mexa64'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML_RAVEN.mexglx'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML_RAVEN.mexmaci64'</span>; fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'TranslateSBML_RAVEN.mexmaca64'</span>);
0332 fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML_RAVEN.mexa64'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML_RAVEN.mexglx'</span>); fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML_RAVEN.mexmaci64'</span>; fullfile(binDir,<span class="string">'libSBML'</span>,<span class="string">'OutputSBML_RAVEN.mexmaca64'</span>);
0333 fullfile(binDir,<span class="string">'mafft'</span>,<span class="string">'mafft-linux64'</span>,<span class="string">'mafft.bat'</span>);
0334 fullfile(binDir,<span class="string">'mafft'</span>,<span class="string">'mafft-mac'</span>,<span class="string">'mafft.bat'</span>);};
0335
0336 <span class="keyword">for</span> i=1:numel(binList)
0337 [status,cmdout] = system([<span class="string">'chmod +x &quot;'</span> binList{i} <span class="string">'&quot;'</span>]);
0338 <span class="keyword">if</span> status ~= 0
0339 warning(<span class="string">'Failed to make %s executable: %s '</span>,binList{i},strip(cmdout))
0340 <span class="keyword">end</span>
0341 <span class="keyword">end</span>
0342 <span class="keyword">end</span>
0343
0344 <a name="_sub4" href="#_subfunctions" class="code">function printOrange(stringToPrint)</a>
0345 <span class="comment">% printOrange</span>
0346 <span class="comment">% Duplicate of RAVEN/core/printOrange is also kept here, as this function</span>
0347 <span class="comment">% should be able to run before adding RAVEN to the MATLAB path.</span>
0348 <span class="keyword">try</span> useDesktop = usejava(<span class="string">'desktop'</span>); <span class="keyword">catch</span>, useDesktop = false; <span class="keyword">end</span>
0349 <span class="keyword">if</span> useDesktop
0350 fprintf([<span class="string">'[\b'</span> stringToPrint,<span class="string">']\b'</span>])
0351 <span class="keyword">else</span>
0352 fprintf(stringToPrint)
0353 <span class="keyword">end</span>
0354 <span class="keyword">end</span></pre></div>
<hr><address>Generated by <strong><a href="http://www.artefact.tk/software/matlab/m2html/" title="Matlab Documentation in HTML">m2html</a></strong> &copy; 2005</address>
</body>
</html>
22 changes: 12 additions & 10 deletions installation/checkInstallation.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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')
Expand Down Expand Up @@ -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');};

Expand Down

0 comments on commit 493ce8d

Please sign in to comment.