I am not sure how to do this.
There is a section in the apache httpd.conf that shows:
Should I just delete either one of the PassEnv WEBSERVER_ROOT? Thanks.
#
# Begin settings for the Trans Proteomic Pipeline
#
# Add 5-hour timeout
Timeout 18000
Alias /tpp-bin "C:/Inetpub/tpp-bin"
<Directory "C:/Inetpub/tpp-bin">
Options Indexes MultiViews ExecCGI
AllowOverride None
Order allow,deny
Allow from all
AddHandler cgi-script .cgi .pl
ScriptInterpreterSource Registry
PassEnv WEBSERVER_ROOT
PassEnv WEBSERVER_TMP
</Directory>
Alias /ISB "C:/Inetpub/wwwroot/ISB"
Alias /schema "C:/Inetpub/wwwroot/schema"
<Directory "C:/Inetpub/wwwroot">
Options Indexes MultiViews Includes
AllowOverride None
Order allow,deny
Allow from all
AddType text/html .shtml
AddHandler server-parsed .shtml
PassEnv WEBSERVER_ROOT
PassEnv WEBSERVER_TMP
</Directory>
#
# End settings for the Trans Proteomic Pipeline
#
On Wed, Mar 10, 2010 at 4:21 PM, Brian Pratt <[email protected]>wrote:
> 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 <[email protected]>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 <[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
>>>>>>> >>>>
>>>>>>> >>>> --
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