Thanks!!. It is working normally now...phew. Lik Wee
On Wed, Mar 10, 2010 at 4:46 PM, Brian Pratt <[email protected]>wrote: > It's a windows thing: ControlPanel|System|Advanced|EnvironmentVariables > > Good luck! > > Brian > > On Wed, Mar 10, 2010 at 4:33 PM, Lik Wee Lee <[email protected]>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 <[email protected] >> > 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 >>> <[email protected]>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 < >>>> [email protected]> wrote: >>>> >>>>> Did you have a working TPP installation before? >>>>> >>>>> On Wed, Mar 10, 2010 at 3:54 PM, Lik Wee Lee < >>>>> [email protected]> wrote: >>>>> >>>>>> Hi Brian, >>>>>> >>>>>> On Wed, Mar 10, 2010 at 3:34 PM, Brian Pratt < >>>>>> [email protected]> 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 < >>>>>>> [email protected]> 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 <[email protected]>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 < >>>>>>>>> [email protected]> 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 < >>>>>>>>> [email protected]> >>>>>>>>> > 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 < >>>>>>>>> [email protected]> >>>>>>>>> >> 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 < >>>>>>>>> [email protected]> >>>>>>>>> >>> 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 >>>>>>>>> [email protected]. >>>>>>>>> >>>> To unsubscribe from this group, send email to >>>>>>>>> >>>> [email protected]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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]<spctools-discuss%[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.
