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. 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