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. 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