Hi Ulrich, Thank you. I was missing the
SetEnv WEBSERVER_TMP /tmp/ from the httpd.conf file. This has been added and after restarting it all works now. Cheers Robert On 08/05/2012, at 6:55 PM, Ulrich auf dem Keller wrote: > Hi Robert, > > from this I would guess WEBSERVER_ROOT is not correctly specified in > httpd.conf. How does your TPP specific section in /etc/apache2/httpd.conf > looks like? > > Here is mine (currently I leave the Mac OS X default > /Library/WebServer/Documents; moving to /thegpm was only kind of laziness to > avoid changing tandem specific scripts at that time): > > #Added for TPP > # ISB-Tools Trans Proteomic Pipeline directive > # > > Alias /tpp/html "/usr/local/tpp/html" > <Directory "/usr/local/tpp/html"> > AllowOverride None > Options Includes FollowSymLinks MultiViews > Order allow,deny > Allow from all > </Directory> > Alias /tpp/schema "/usr/local/tpp/schema" > <Directory "/usr/local/tpp/schema"> > AllowOverride None > Options Includes FollowSymLinks MultiViews > Order allow,deny > Allow from all > </Directory> > Alias /tpp/tpp_data "/Library/WebServer/Documents/tpp/tpp_data" > <Directory "/Library/WebServer/Documents/tpp/tpp_data"> > AllowOverride None > Options Includes Indexes FollowSymLinks MultiViews > Order allow,deny > Allow from all > </Directory> > Alias /tpp/cgi-bin "/usr/local/tpp/cgi-bin" > <Directory "/usr/local/tpp/cgi-bin"> > AllowOverride None > Options ExecCGI > Order allow,deny > Allow from all > SetEnv WEBSERVER_ROOT /Library/WebServer/Documents/ > SetEnv WEBSERVER_URL http://localhost/ > SetEnv WEBSERVER_TMP /tmp/ > </Directory> > > Don't forget the restart apache after applying any changes. > > Best, > > Ulrich > > On 2012-05-08, at 2:24 AM, Robert Willows wrote: > >> Hi Ulrich, >> >> I've checked the $tmp_dir and this is OK as the tpp log file and cmd files >> are being written to the tmp folder by '_www' . >> >> I've looked again at the output from running InteractParser from the command >> line compared to running from the web server and it seems the output files >> from the web server have had the path info stripped and are written as >> //interact.pep.xml.tmp with two leading "/" when it fails. When run from the >> command line the output files have the full path specified e.g. >> "/Library/WebServer/Documents/thegpm/tpp/data/interact.pep.shtml" The output >> files are written to whatever directory the command is run from, including >> the tmp files which can be seen if the process is halted part way through. >> >> The problem could be related to how the outfile is specified in the >> InteractParser.cxx file (Lines 179-228). If the WebserverRoot is part of the >> path to the outfile then this is stripped and the trailing "/" is retained >> but I think that '_www' then tries to write to the path >> "//interact.pep.xml.tmp". The double "/" is not allowed and the file can't >> be created. >> From the command line this doesn't happen since the whole path is retained >> because WEBSERVER_ROOT is not an environment variable in a bash terminal. >> >> If this is the problem I'm not sure how to fix it since I'm not that >> familiar with C++. >> >> Regards >> Robert >> >> On 08/05/2012, at 4:03 AM, Luis Mendoza wrote: >> >>> Hi Ulrich, >>> Thanks for reporting the bug in Petunia. It will be fixed as of the >>> next upcoming release, 4.6.0. Let me know if you find any others, and >>> thanks again for the Mac support! >>> --Luis >>> >>> >>> On Sat, May 5, 2012 at 3:14 AM, Ulrich auf dem Keller <[email protected]> >>> wrote: >>>> Hi Robert, >>>> >>>> it seems that the _www user doesn't have write permissions for the tmp >>>> folder you specified. When running from command line the commands will be >>>> executed by the user logged into the shell, but from Petunia it will be >>>> '_www' . What's your '$tmp_dir' and its permission settings? Have you set >>>> '$www_root' correctly? It should not be necessary to change anything in >>>> tpp_gui.pl other than in the config section (via tpp_gui_config.pl) or >>>> maybe >>>> in %command. >>>> >>>> The only bug I found in tpp_gui.pl is that lines 2070 - 2072: >>>> >>>> if (param('c_semi')) { >>>> param('c_enzyme', "semi".param('c_enzyme')); >>>> } >>>> >>>> have to moved up out of the for loop before line 2063 to convert multiple >>>> files with 'semi' enzyme definition. >>>> >>>> Hope that helps. >>>> >>>> Cheers >>>> >>>> Ulrich >>>> >>>> On 2012-05-03, at 5:49 AM, Robert Willows wrote: >>>> >>>> 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. >>>> >>>> >>>> -- >>>> 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. >>> >>> -- >>> 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. >>> >> >> -- >> 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. >> > > -- > 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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