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 >>>>>> >>>> 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