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. 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