It's a windows thing: ControlPanel|System|Advanced|EnvironmentVariables Good luck!
Brian On Wed, Mar 10, 2010 at 4:33 PM, Lik Wee Lee <l...@systemsbiology.org>wrote: > I am not sure how to do this. > There is a section in the apache httpd.conf that shows: > Should I just delete either one of the PassEnv WEBSERVER_ROOT? Thanks. > > # > # Begin settings for the Trans Proteomic Pipeline > # > > # Add 5-hour timeout > Timeout 18000 > > 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 > # > > On Wed, Mar 10, 2010 at 4:21 PM, Brian Pratt > <brian.pr...@insilicos.com>wrote: > >> ah, wait, I do see one weird thing: >> >> WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot >> >> change that environment variable to >> >> WEBSERVER_ROOT = c:\Inetpub\wwwroot >> >> and see how it goes. >> >> On Wed, Mar 10, 2010 at 4:18 PM, Lik Wee Lee >> <l...@systemsbiology.org>wrote: >> >>> Nope. I installed it recently and it complained about missing perl so I >>> downloaded 5.10 and installed it successfully. >>> But when I ran into problems, I thought it might be due to the perl >>> version, so I uninstall Perl 5.10.1 and TPP and then reinstall Perl 5.8.9 >>> and TPP. >>> >>> Lik Wee >>> >>> On Wed, Mar 10, 2010 at 4:08 PM, Brian Pratt < >>> brian.pr...@insilicos.com> wrote: >>> >>>> Did you have a working TPP installation before? >>>> >>>> On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee <l...@systemsbiology.org >>>> > wrote: >>>> >>>>> Hi Brian, >>>>> >>>>> On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt < >>>>> brian.pr...@insilicos.com> wrote: >>>>> >>>>>> I think the fact that run_in doesn't work indicates some kind of >>>>>> system level problem that's going to make everything else flaky. Perl >>>>>> shouldn't be an issue, at least at this point. >>>>>> >>>>>> So "c:\inetpub\tpp-bin\run_in c:\; dir" doesn't work for you? >>>>>> >>>>> >>>>> I still get command "dir" failed: Unknown error >>>>> >>>>>> >>>>>> What do you see when you type this into your browser address bar? >>>>>> http://localhost/tpp-bin/check_env.pl >>>>>> >>>>>> >>>>> >>>>> SCRIPT_NAME = /tpp-bin/check_env.pl >>>>> SERVER_NAME = localhost >>>>> HTTP_ACCEPT_ENCODING = gzip,deflate >>>>> HTTP_CONNECTION = keep-alive >>>>> REQUEST_METHOD = GET >>>>> SYSTEMROOT = C:\WINDOWS >>>>> HTTP_ACCEPT = >>>>> text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8 >>>>> SCRIPT_FILENAME = C:/Inetpub/tpp-bin/check_env.pl >>>>> COMSPEC = C:\WINDOWS\system32\cmd.exe >>>>> SERVER_SOFTWARE = Apache/2.2.8 (Win32) >>>>> HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 >>>>> WINDIR = C:\WINDOWS >>>>> QUERY_STRING = >>>>> REMOTE_PORT = 3227 >>>>> PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH >>>>> HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; >>>>> rv:1.9.0.18) Gecko/2010020220 Firefox/3.0.18 (.NET CLR 3.5.30729) >>>>> SERVER_PORT = 80 >>>>> SERVER_SIGNATURE = >>>>> HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 >>>>> HTTP_COOKIE = >>>>> TPPSession=TYBEEDEHS:guest:249069786675ffea98006f8c1b444fa1 >>>>> REMOTE_ADDR = 127.0.0.1 >>>>> WEBSERVER_ROOT = c:\Inetpub\wwwroot;c:\Inetpub\wwwroot >>>>> HTTP_KEEP_ALIVE = 300 >>>>> SERVER_PROTOCOL = HTTP/1.1 >>>>> PATH = C:\Inetpub\tpp-bin;C:\Xcalibur\system\programs;C:\Program >>>>> Files\Thermo\Foundation;C:\Perl\site\bin;C:\Perl\bin;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program >>>>> Files\Common Files\Adaptec Shared\System;C:\Program Files\Analyst\bin >>>>> REQUEST_URI = /tpp-bin/check_env.pl >>>>> GATEWAY_INTERFACE = CGI/1.1 >>>>> SERVER_ADDR = 127.0.0.1 >>>>> DOCUMENT_ROOT = C:/Program Files/Apache Software >>>>> Foundation/Apache2.2/htdocs >>>>> HTTP_HOST = localhost >>>>> >>>>> Thanks for your help, >>>>> Lik Wee >>>>> >>>>> >>>>>> It should give you a bunch of info including the PATH setting for >>>>>> your webserver. >>>>>> >>>>>> On Wed, Mar 10, 2010 at 2:47 PM, Lik Wee Lee < >>>>>> l...@systemsbiology.org> wrote: >>>>>> >>>>>>> Hi Jimmy, >>>>>>> >>>>>>> Yes, I also checked the .tandem file there were peptides with low >>>>>>> expect score. >>>>>>> I also looked at the .pep.xml file and checked that the scans, >>>>>>> hyperscore, >>>>>>> nextscore, bscore, ... matched the .tandem file. >>>>>>> >>>>>>> I am puzzled why the run_in doesn't work and wondering if this is >>>>>>> affecting >>>>>>> the xinteract command as well. any ideas? >>>>>>> >>>>>>> Lik Wee >>>>>>> >>>>>>> >>>>>>> On Wed, Mar 10, 2010 at 2:20 PM, Jimmy Eng <jke...@gmail.com> wrote: >>>>>>> >>>>>>>> I suggest you start debugging the problem one step at a time. >>>>>>>> First confirm that your Tandem search actually ran by looking at >>>>>>>> contents of the .tandem file. >>>>>>>> Next, check contents of tandem.pep.xml. >>>>>>>> Do both of these files look like they have peptide IDs in them? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Wed, Mar 10, 2010 at 2:04 PM, Lik Wee Lee < >>>>>>>> l...@systemsbiology.org> wrote: >>>>>>>> > Furthermore, I also did: >>>>>>>> > C:\Inetpub\wwwroot\ISB\data\17mix>c:\Inetpub\tpp-bin\Tandem2XML >>>>>>>> > >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem >>>>>>>> > >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml >>>>>>>> > >>>>>>>> > but if I tried to browse file in petunia and click on [PepXML], >>>>>>>> > it opens a new window: >>>>>>>> > >>>>>>>> http://localhost/tpp-bin/PepXMLViewer.cgi?xmlFileName=c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml >>>>>>>> > >>>>>>>> > but with the message: >>>>>>>> > >>>>>>>> > error: >>>>>>>> > can't open html >>>>>>>> > >>>>>>>> templatec:/Inetpub/wwwroot;c:/Inetpub/wwwroot/ISB/html/PepXMLViewer.html >>>>>>>> > >>>>>>>> > I also had problem with xinteract: >>>>>>>> > >>>>>>>> > >>>>>>>> C:\Inetpub\wwwroot\ISB\data\17mix\tandem>c:\Inetpub\tpp-bin\xinteract >>>>>>>> > -Ninteract.pep.xml -p0.05 -l7 -O >>>>>>>> > >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.pep.xml >>>>>>>> > >>>>>>>> > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build >>>>>>>> 200909091257 >>>>>>>> > (MinGW)) >>>>>>>> > >>>>>>>> > running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >>>>>>>> > "c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tand >>>>>>>> > em.pep.xml" -L"7"" >>>>>>>> > >>>>>>>> > command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >>>>>>>> > >>>>>>>> "c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande >>>>>>>> > m.pep.xml" -L"7"" failed: Unknown error >>>>>>>> > >>>>>>>> > command "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" >>>>>>>> > >>>>>>>> "c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tande >>>>>>>> > m.pep.xml" -L"7"" exited with non-zero exit code: -1 >>>>>>>> > QUIT - the job is incomplete >>>>>>>> > >>>>>>>> > >>>>>>>> > >>>>>>>> > Is this an installation issue? Any ideas? >>>>>>>> > >>>>>>>> > Thanks, >>>>>>>> > Lik Wee >>>>>>>> > >>>>>>>> > On Wed, Mar 10, 2010 at 1:53 PM, Lik Wee Lee < >>>>>>>> l...@systemsbiology.org> >>>>>>>> > wrote: >>>>>>>> >> >>>>>>>> >> Hi Brian, >>>>>>>> >> >>>>>>>> >> The full path still gives command "..." failed: unknown error. >>>>>>>> >> >>>>>>>> >> I tried "run_in c:" and didn't get any output. >>>>>>>> >> >>>>>>>> >> But if I try "run_in c:\; dir", I get: >>>>>>>> >> command "dir" failed: Unknown error. >>>>>>>> >> >>>>>>>> >> Could it be I previously had installed Perl 5.10? I uninstalled >>>>>>>> it >>>>>>>> >> and then installed Perl 5.8.9 followed by tpp 4.3.1. >>>>>>>> >> >>>>>>>> >> Lik Wee >>>>>>>> >> >>>>>>>> >> On Wed, Mar 10, 2010 at 1:34 PM, Brian Pratt < >>>>>>>> brian.pr...@insilicos.com> >>>>>>>> >> wrote: >>>>>>>> >>> >>>>>>>> >>> "run_in" is just a little program that runs one or more commands >>>>>>>> in the >>>>>>>> >>> indicated directory. For example "run_in c:\foo; bar.exe; >>>>>>>> baz.exe" performs >>>>>>>> >>> "cd c:\foo" then runs "bar.exe" then "baz.exe". It exists to >>>>>>>> help with >>>>>>>> >>> linux-oriented multipart command lines in the GUI, statements >>>>>>>> like "cd >>>>>>>> >>> c:foo; bar.exe; baz.exe" (we just swap "run_in" for "cd" on the >>>>>>>> windows >>>>>>>> >>> installation). >>>>>>>> >>> >>>>>>>> >>> Anyway, that's what it's for - why it doesn't work for you is a >>>>>>>> mystery. >>>>>>>> >>> Perhaps it's a path issue: how does the command line >>>>>>>> >>> c:\Inetpub\tpp-bin\run_in >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem; >>>>>>>> >>> c:\Inetpub\tpp-bin\tandem >>>>>>>> >>> >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params >>>>>>>> >>> >>>>>>>> >>> work for you (that is, with full path to run_in specified)? >>>>>>>> >>> >>>>>>>> >>> On Wed, Mar 10, 2010 at 1:21 PM, Lik Wee Lee < >>>>>>>> l...@systemsbiology.org> >>>>>>>> >>> wrote: >>>>>>>> >>>> >>>>>>>> >>>> Hi, >>>>>>>> >>>> >>>>>>>> >>>> When I tried to do a xtandem search in the TPP petunia >>>>>>>> interface, >>>>>>>> >>>> I encountered the problem: >>>>>>>> >>>> >>>>>>>> >>>> # Commands for session TYBEEDEHS on Wed Mar 10 13:13:38 2010 >>>>>>>> >>>> # BEGIN COMMAND BLOCK >>>>>>>> >>>> ###### BEGIN Command Execution ###### >>>>>>>> >>>> >>>>>>>> >>>> [Wed Mar 10 13:13:38 2010] EXECUTING: run_in >>>>>>>> >>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem; >>>>>>>> c:\Inetpub\tpp-bin\tandem >>>>>>>> >>>> >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params >>>>>>>> >>>> OUTPUT: >>>>>>>> >>>> >>>>>>>> >>>> command "c:\Inetpub\tpp-bin\tandem >>>>>>>> >>>> >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params" >>>>>>>> >>>> failed: Unknown error >>>>>>>> >>>> >>>>>>>> >>>> >>>>>>>> >>>> >>>>>>>> >>>> >>>>>>>> >>>> END OUTPUT >>>>>>>> >>>> RETURN CODE:65280 >>>>>>>> >>>> ###### End Command Execution ###### >>>>>>>> >>>> # All finished at Wed Mar 10 13:13:38 2010 >>>>>>>> >>>> # END COMMAND BLOCK >>>>>>>> >>>> >>>>>>>> >>>> Does anyone have any ideas why this occur? >>>>>>>> >>>> However, the search was performed successfully if I did it by >>>>>>>> command >>>>>>>> >>>> line: >>>>>>>> >>>> >>>>>>>> >>>> c:\Inetpub\tpp-bin\tandem >>>>>>>> >>>> >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params >>>>>>>> >>>> >>>>>>>> >>>> If I try >>>>>>>> >>>> >>>>>>>> >>>> run_in c:/Inetpub/wwwroot/ISB/data/17mix/tandem; >>>>>>>> >>>> c:\Inetpub\tpp-bin\tandem >>>>>>>> >>>> >>>>>>>> c:/Inetpub/wwwroot/ISB/data/17mix/tandem/OR20091211_18mix_01.tandem.params >>>>>>>> >>>> >>>>>>>> >>>> it says command failed: Unknown error. >>>>>>>> >>>> >>>>>>>> >>>> I have ActivePerl 5.8.9 build 827 and TPP version 4.3.1 >>>>>>>> installed on >>>>>>>> >>>> Windows XP SP3. >>>>>>>> >>>> >>>>>>>> >>>> Thanks, >>>>>>>> >>>> Lik Wee >>>>>>>> >>>> >>>>>>>> >>>> -- >>>>>>>> >>>> You received this message because you are subscribed to the >>>>>>>> Google >>>>>>>> >>>> Groups "spctools-discuss" group. >>>>>>>> >>>> To post to this group, send email to >>>>>>>> spctools-disc...@googlegroups.com. >>>>>>>> >>>> To unsubscribe from this group, send email to >>>>>>>> >>>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>>>>>>> >>> To post to this group, send email to >>>>>>>> spctools-disc...@googlegroups.com. >>>>>>>> >>> To unsubscribe from this group, send email to >>>>>>>> >>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>>>>>>> > To post to this group, send email to >>>>>>>> spctools-disc...@googlegroups.com. >>>>>>>> > To unsubscribe from this group, send email to >>>>>>>> > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>>>>>>> To post to this group, send email to >>>>>>>> spctools-disc...@googlegroups.com. >>>>>>>> To unsubscribe from this group, send email to >>>>>>>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>>>>>> To post to this group, send email to >>>>>>> spctools-disc...@googlegroups.com. >>>>>>> To unsubscribe from this group, send email to >>>>>>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>>>>> To post to this group, send email to >>>>>> spctools-disc...@googlegroups.com. >>>>>> To unsubscribe from this group, send email to >>>>>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>>>> 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<spctools-discuss%2bunsubscr...@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. >>>> To post to this group, send email to spctools-disc...@googlegroups.com. >>>> To unsubscribe from this group, send email to >>>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >>> To post to this group, send email to spctools-disc...@googlegroups.com. >>> To unsubscribe from this group, send email to >>> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. >> To post to this group, send email to spctools-disc...@googlegroups.com. >> To unsubscribe from this group, send email to >> spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. > To post to this group, send email to spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@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. To post to this group, send email to spctools-disc...@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.
