Dear TPP team, I've just finished installing TPP Rapture Rev 2 on Max OSX 10.7.3. with some success, although some of the functions don't work through the Web interface but the same commands work on on the command line.
I used the instructions at: http://tools.proteomecenter.org/wiki/index.php?title=The_Trans_Proteomic_Pipeline_%28TPP%29_for_Mac_OS_X_10.6.4 I also need to modify the endian.hpp file as per instructions from the post by Ulrich below: Workaround is to comment out conditions for LITTLE_ENDIAN in /extern/ProteoWizard/pwiz/pwiz/utility/misc/endian.hpp: change to: // #if (defined(PWIZ_GCC) && defined(__BYTE_ORDER) && __BYTE_ORDER==__LITTLE_ENDIAN) || \ // (defined(__DARWIN_BYTE_ORDER) && __DARWIN_BYTE_ORDER==__DARWIN_LITTLE_ENDIAN) || \ // (defined(__DARWIN_10_6_AND_LATER) && defined(__LITTLE_ENDIAN__)) || \ // (defined(__MINGW32__)) || \ // (defined(__i386__)) || \ // (defined(PWIZ_MSVC)) #define PWIZ_LITTLE_ENDIAN // #endif I needed to comment out the path stripping in tpp_gui.pl to get xinteract to work, or at least generate a command which would work at the command line. So on line 2008-2011 was commented out as below and an extra line added without the path stripping: # my @file_list_stripped = &stripPaths(files => \@file_list, # bpath =>$outd); #$command = "$command{chdir} $outd; $command{xinteract} $options @file_list_stripped"; $command = "$command{chdir} $outd; $command{xinteract} $options @file_list"; This generates a command e.g. /usr/bin/cd /Library/WebServer/Documents/thegpm/tpp/data; /usr/local/tpp/bin/xinteract -Ninteract.pep.xml -p0.05 -l7 -O /Library/WebServer/Documents/thegpm/tpp/data/XXXXX.tandem.pep.xml However I get the following on the Web interface: /usr/local/tpp/bin/xinteract (TPP v4.5 RAPTURE rev 2, Build 201204271337 (linux)) running: "/usr/local/tpp/bin/InteractParser 'interact.pep.xml' '/Library/WebServer/Documents/thegpm/tpp/data/XXXXX.tandem.pep.xml' -L'7'" cannot write output to file //interact.pep.xml.tmp.AndtL8 command "/usr/local/tpp/bin/InteractParser 'interact.pep.xml' '/Library/WebServer/Documents/thegpm/tpp/data/XXXXX.tandem.pep.xml' -L'7'" exited with non-zero exit code: 256 QUIT - the job is incomplete Command FAILED However, when I cut and paste the same command at the command line it works fine. Also other options used with xinteract also all work and the files are generated as expected and can be viewed through the web interface. I'm not sure where InteractParser is trying to write the tmp file but maybe this is the problem? Regards Robert -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
