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. 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