Hi Vishal and all, The only log file I see in C:\tmp is a tpp_web.log file and it contains 2 lines Cannot run user command; previous still running Cannot run user command; previous still running
I am not sure which Apache log you are talking about. Below is a snippet of some lines from my error.log inside Apache's log folder: [Fri Oct 21 10:14:39 2011] [warn] pid file C:/Program Files/Apache Software Foundation/Apache2.2/logs/httpd.pid overwritten -- Unclean shutdown of previous Apache run? [Fri Oct 21 10:14:39 2011] [notice] Apache/2.2.8 (Win32) configured -- resuming normal operations [Fri Oct 21 10:14:39 2011] [notice] Server built: Jan 18 2008 00:37:19 [Fri Oct 21 10:14:39 2011] [notice] Parent: Created child process 1684 [Fri Oct 21 10:14:39 2011] [notice] Child 1684: Child process is running [Fri Oct 21 10:14:39 2011] [notice] Child 1684: Acquired the start mutex. [Fri Oct 21 10:14:39 2011] [notice] Child 1684: Starting 250 worker threads. [Fri Oct 21 10:14:39 2011] [notice] Child 1684: Starting thread to listen on port 8080. [Fri Oct 21 10:17:13 2011] [error] [client 127.0.0.1] Premature end of script headers: PepXMLViewer.cgi, referer: http://localhost:8080/tpp-bin/tpp_gui.pl?Action=display&page=filebrowser&file_ext=*&workdir=c:/Inetpub/wwwroot/ISB/data/demo2009//tandem [Tue Oct 25 14:31:39 2011] [error] [client 127.0.0.1] Premature end of script headers: test.cgi [Tue Oct 25 14:35:32 2011] [error] [client 127.0.0.1] Premature end of script headers: test.cgi As you can see above it also recorded my attempt of opening the test.cgi file that you instructed me to create, which resulted in the same Internal Server Error screen. I see two copies of ActivePerl, one with build 5.8.4 and one with 5.12.4 so I uninstalled then 5.8.4 version, which did not help solve the problem. Most folders in my previous PATH value do not exist anymore, and I have deleted any folder that contains perl other than my currently installed perl directory. I may need to do another fresh install of perl and/or TPP because even GUI gives me the internal server error screen now. Thanks for any other tips. Regards, Chris On Oct 23, 6:36 pm, Vishal Swaroop <vishal....@gmail.com> wrote: > Hi Chris, > > In this URLhttp://flic.kr/p/axzsk8there are multiple files, TPP log shows > some permission issue. > > Can you try fresh and send the latest log file from "C:\tmp" and see if > there is any thing in Apache logs ? > > Please check if simple CGI works... > Create "test.cgi" under "C:\Inetpub\tpp-bin" and add this content, the try > http:/localhost:8080/tpp-bin/test.cgi > #!C:/Perl/bin/perl > print "Content-type:text/html\n\n"; > print "OK"; > > Also, looks like there are multiple installation of perl as per your path... > > > > > > > > On Fri, Oct 21, 2011 at 1:23 PM, Chris L <li...@uci.edu> wrote: > > Hi Vishal and all, > > I am doing step 7: "Visualize LC-MS/MS data using Pep3D " in TPP Demo > > 2009 (http://tools.proteomecenter.org/wiki/index.php? > > title=TPP_Demo2009) > > a) I had C:\tmp to begin with > > b) I am using firefox. I tried to open it with IE6 and encountered the > > same problem. > > c) I did not have user variable WEBSERVER_ROOT and had to create one > > I had PATH's value as > > C:\Inetpub\tpp-bin;C:\Program Files\Perl\site\bin;C:\Program Files\Perl > > \bin;C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C: > > \cygwin\usr\X11R6\bin;C:\cygwin\bin;C:\Perl\site\bin;C:\Perl\bin;J: > > \oracle\ora92\bin;C:\Program Files\Oracle\jre\1.1.8\bin;C:\Perl\bin; > > %SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;C: > > \Program Files\Intel\DMIX;C:\cygwin\usr\X11R6\bin;C:\cygwin\bin;C: > > \Program Files\QuickTime\QTSystem\;C:\strawberry\c\bin;C:\strawberry > > \perl\site\bin;C:\strawberry\perl\bin > > so I changed it to yours, and rebooted the computer, which still did > > not solve the problem. > > d) Heres my snippet of "httpd.conf" in Apache > > # > > # Begin settings for the Trans Proteomic Pipeline > > # > > Alias /tpp-bin "C:/Inetpub/tpp-bin" > > <Directory "C:/Inetpub/tpp-bin"> > > Options Indexes MultiViews ExecCGI > > AllowOverride None > > Order allow,deny > > Allow from all > > > AddHandler cgi-script .cgi .pl > > ScriptInterpreterSource Registry > > > PassEnv WEBSERVER_ROOT > > PassEnv WEBSERVER_TMP > > </Directory> > > > Alias /ISB "C:/Inetpub/wwwroot/ISB" > > > Alias /schema "C:/Inetpub/wwwroot/schema" > > > <Directory "C:/Inetpub/wwwroot"> > > Options Indexes MultiViews Includes > > AllowOverride None > > Order allow,deny > > Allow from all > > > AddType text/html .shtml > > AddHandler server-parsed .shtml > > > PassEnv WEBSERVER_ROOT > > PassEnv WEBSERVER_TMP > > </Directory> > > # > > # End settings for the Trans Proteomic Pipeline > > # > > > Thanks in advance for your advices. > > > Regards, > > Chris > > > On Oct 20, 5:39 pm, Vishal Swaroop <vishal....@gmail.com> wrote: > > > Hi Chris, > > > > Good to know that it worked.. > > > > I am not sure about step7 (please send me the url you are referring). > > > > I am sure there were lot of things dependent on OS.. may be try this... > > > restart after if changing variables as I think System variable change > > > requires restart but not user variable change... so just re-start.. :) > > > > a) I assume you have default data directory i.e. "C:" Check if you have > > > "C:\tmp", if not then create it. > > > b) Which browser you are using, I am using IE8 and it works fine. > > > c) Right click : "My Computer">Properties>Advanced Tab> Environment > > > variables > > > Check User variable : > > > Variable name : WEBSERVER_ROOT > > > Variable value : C:\Inetpub\wwwroot > > > > Check System Variables : > > > Variable name "PATH" should have > > > C:\Inetpub\tpp-bin;C:\Perl\site\bin;C:\Perl\bin; > > > > d) Here is snippet of Apache "httpd.conf" file which you can compare.. > > > > # > > > # Begin settings for the Trans Proteomic Pipeline > > > # > > > > # Add 5-hour timeout > > > Timeout 18000 > > > > AddType text/html .shtml > > > AddHandler server-parsed .shtml > > > > SetEnv WEBSERVER_ROOT C:/Inetpub/wwwroot > > > SetEnv WEBSERVER_URLhttp://localhost:81 > > > > Alias /tpp-bin "C:/Inetpub/tpp-bin" > > > <Directory "C:/Inetpub/tpp-bin"> > > > Options Indexes MultiViews ExecCGI > > > AllowOverride None > > > Order allow,deny > > > Allow from all > > > > AddHandler cgi-script .cgi .pl > > > ScriptInterpreterSource Registry > > > PassEnv WEBSERVER_ROOT > > > </Directory> > > > > Alias /ISB "C:/Inetpub/wwwroot/ISB" > > > Alias /isb "C:/Inetpub/wwwroot/ISB" > > > <Directory "C:/Inetpub/wwwroot/ISB"> > > > Options Indexes MultiViews Includes ExecCGI > > > AllowOverride None > > > Order allow,deny > > > Allow from all > > > > AddType text/html .shtml > > > AddHandler server-parsed .shtml > > > PassEnv WEBSERVER_ROOT > > > </Directory> > > > > On Thu, Oct 20, 2011 at 7:02 PM, Chris L <li...@uci.edu> wrote: > > > > Hi all, > > > > I am still encountering problem with tutorial step 6 which I am > > > > ignoring for now. > > > > In step 7, I am not able to open pepXML viewer for my interact.pep.xml > > > > and here's the screen I get when trying to open it: > > > >http://flic.kr/p/axzsk8 > > > > Any tip appreciated. Thanks again. > > > > > Regards, > > > > Chris > > > > > On Oct 20, 3:39 pm, Chris L <li...@uci.edu> wrote: > > > > > Changing the domain to localhost:8080 solved the problem. > > > > > Thanks a lot Vishal. > > > > > > Regards, > > > > > Chris > > > > > > On Oct 19, 6:55 am, Vishal Swaroop <vishal....@gmail.com> wrote: > > > > > > > Which browser you are using, firefox ?, try using IE or other > > > > > > > First check if Apache is configured correctly, tryhttp://localhost, > > you > > > > > > should see "It works!" message on browser, if you have port other > > than > > > > > > default (80) then usehttp://localhost:<your port> > > > > > > > Then try http://<localhost>:<port>/tpp-bin/tpp_gui.pl, if you have > > not > > > > > > changed the port then it should be > > > >http://localhost/tpp-bin/tpp_gui.pl > > > > > > > ..\Apache...\conf\httpd.conf should have information of host and > > port. > > > > > > > Hope this helps.. > > > > > > > On Tue, Oct 18, 2011 at 7:46 PM, Chris L <li...@uci.edu> wrote: > > > > > > > localhost/tpp-bin/tpp_gui.pl > > > > > > > > The web browser changes it towww.localhost.comautomatically. > > > > > > > > Chris > > > > > > > > On Oct 18, 4:44 pm, Chris L <li...@uci.edu> wrote: > > > > > > > > No, I havehttp://www.localhost.com/tpp-bin/tpp_gui.pl > > > > > > > > Formatting of my post caused the confusion > > > > > > > > > Regards, > > > > > > > > Chris > > > > > > > > > On Oct 18, 4:19 pm, "Vensel, William" < > > william.ven...@ars.usda.gov > > > > > > > > > wrote: > > > > > > > > > > Hi Chris, > > > > > > > > > > Is there a blank space in yur web address? // Local vs > > //local > > > > > > > > > > Bill > > > > > > > > > > -----Original Message----- > > > > > > > > > From: spctools-discuss@googlegroups.com [mailto: > > > > > > > spctools-discuss@googlegroups.com] On Behalf Of Chris L > > > > > > > > > Sent: Tuesday, October 18, 2011 3:28 PM > > > > > > > > > To: spctools-discuss > > > > > > > > > Subject: [spctools-discuss] Re: TPP Demo 2009 > > > > > > > > > > Hi Luis and all, > > > > > > > > > > I have uninstalled Microsoft IIS from the windows component > > > > (running > > > > > > > > > windows XP) and re-installed TPP v4.5 with the default Apache > > > > > > > > > webserver. Now the problem is when I try to access the GUI > > > > (http:// > > > > > > > > > localhost/tpp-bin/tpp_gui.pl), I get a blank page. > > Refreshing > > > > the page > > > > > > > > > and rebooting doesn't help. Any tips and advice appreciated. > > > > > > > > > > Sorry for all the miniscule questions and thanks again for > > being > > > > > > > > > patient. > > > > > > > > > > Regards, > > > > > > > > > Chris > > > > > > > > > > On Oct 14, 4:11 pm, Luis Mendoza < > > > > luis.mend...@systemsbiology.org> > > > > > > > > > wrote: > > > > > > > > > > Hello Chris, > > > > > > > > > > From the "timeout" error screenshot, it seems that you are > > > > using the > > > > > > > IIS > > > > > > > > > > server. The TPP does not support this web server; instead > > we > > > > > > > recommend that > > > > > > > > > > you install and run the Apache web server -- which is > > bundled > > > > and > > > > > > > installed > > > > > > > > > > with the TPP (provided you check the default boxes in the > > > > install > > > > > > > wizard). > > > > > > > > > > > Hope this helps, > > > > > > > > > > --Luis > > > > > > > > > > > On Fri, Oct 14, 2011 at 4:04 PM, Chris L <li...@uci.edu> > > > > wrote: > > > > > > > > > > > Dear all, > > > > > > > > > > > > I am experimenting with the TPP demo 2009 (http:// > > > tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009) > > > > and > > > > > > > > > > > encountered two problems. > > > > > > > > > > > > First, for step 6: Validation of Peptide-Spectrum > > assignments > > > > with > > > > > > > > > > > PeptideProphet, I can never get past the Run XInteract > > step. > > > > My > > > > > > > > > > > command does not finish running even after over a day! > > > > (screen: > > > > > > > > > > >http://flic.kr/p/avNB4R) > > > > > > > > > > > > Second, when I am trying step 7: Visualize LC-MS/MS data > > > > using > > > > > > > Pep3D. > > > > > > > > > > > My browser tab shows "Connecting..." and a blank page > > that > > > > does not > > > > > > > > > > > load and eventually turns into a CGI error page (screen: > > > > > > > > > > >http://flic.kr/p/avNAXk) > > > > > > > > > > > > Any suggestion appreciated. Thank you. > > > > > > > > > > > > Regards, > > > > > > > > > > > Chris > > > > > > > > > > > > -- > > > > > > > > > > > You received this message because you are subscribed to > > the > > > > Google > > > > > > > Groups > > > > > > > > > > > "spctools-discuss" group. > > > > > > > > > > > To post to this group, send email to > > > > > > > spctools-discuss@googlegroups.com. > > > > > > > > > > > To unsubscribe from this group, send email to > > > > > > > > > > > spctools-discuss+unsubscr...@googlegroups.com. > > > > > > > > > > > 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. > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
