David is right... here is snippet from my last post
Environment settings :
- My Computer (right click) > Properties > Advanced system settings >
Advanced (Tab) > Environment Variables
Under *System variable* I have
*WEBSERVER_ROOT *: c:\Inetpub\wwwroot
*Path *: C:\Inetpub\tpp-bin;C:\Perl\site\bin;C:\Perl\bin;
Note : If you are adding under *System variable *then restart for changes
to take effect.
- htppd.conf settings :
# 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 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, Apr 2, 2014 at 1:50 PM, David Shteynberg <
[email protected]> wrote:
> Jason,
>
> Try this:
>
> Right Click "My Computer" -> Properties -> Advanced System Settings ->
> Advanced-> Environment Variables
>
> Here add a *System* variable
>
> WEBSERVER_ROOT c:\Inetpub\wwwroot
>
> Also here make sure that *Path* variable includes c:\Inetpub\tpp-bin and
> also your Perl installation usually c:\Perl\bin
>
> You may need to reboot or restart Apache in order for the setting to take
> effect.
>
> This is meant to be set by the installer but is not always possible on all
> systems. You can see the environment variables set in Apache by going to:
> http://localhost/tpp-bin/check_env.pl
>
>
> Let us know if you need further assistance.
>
>
> -David
>
>
>
>
>
> On Wed, Apr 2, 2014 at 9:22 AM, Vishal Swaroop <[email protected]>wrote:
>
>> Hi Jason,
>>
>> Not sure but this might help
>> https://groups.google.com/forum/#!topic/spctools-discuss/QSUZQ3ViRoQ
>>
>> Thanks
>>
>>
>> On Wed, Apr 2, 2014 at 5:55 AM, jason cao <[email protected]>wrote:
>>
>>> I am struggling to make TPP 4.7 working in Windows 8.
>>>
>>> I am follow the description of " Quick Start to data
>>> analysis using the TPP"（
>>> http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial）.Step1
>>> - step5 is Ok！ Mistakes is happen in step6 ---Validation of
>>> Peptide-Spectrum assignments with PeptideProphet.
>>>
>>> When i *Run XInteract.*The commends finished immediately,and
>>> showed *Command FAILED *RETURN CODE:256.
>>>
>>> Next is the advice and the context of failed commends :
>>>
>>> (I have set the environment variable to my computer,the outcme
>>> still wrong.Plz help me ,thank you ! )
>>>
>>> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml"
>>> "OR20080317_S_SILAC-LH_1-1_01.tandem.pep.xml"
>>> "OR20080320_S_SILAC-LH_1-1_11.tandem.pep.xml" -L"7""
>>>
>>> *<PRE> Environment variable WEBSERVER_ROOT does not exist.
>>>
>>> For Windows users, you can set this environment variable
>>> through the Advanced tab under System Properties when you
>>> right-mouse-click on your My Computer icon.
>>>
>>> Set this environment variable to your webserver's document
>>> root directory such as c:\inetpub\wwwroot for IIS or
>>> c:\website\htdocs or WebSite Pro.
>>>
>>> Exiting.
>>> command completed in 1.39643e+009 sec
>>>
>>> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
>>> pipe "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml"" failed: No error
>>> error, could not execute: C:/Inetpub/tpp-bin/DatabaseParser
>>> "interact.pep.xml"
>>>
>>> command "c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7 -OA
>>> OR20080317_S_SILAC-LH_1-1_01.tandem.pep.xml
>>> OR20080320_S_SILAC-LH_1-1_11.tandem.pep.xml" failed: Operation not
>>> permitted*
>>>
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