Hi Vishal and all,
I am doing step 7: "Visualize LC-MS/MS data using Pep3D " in TPP Demo
2009 (http://tools.proteomecenter.org/wiki/index.php?
title=TPP_Demo2009)
a) I had C:\tmp to begin with
b) I am using firefox. I tried to open it with IE6 and encountered the
same problem.
c) I did not have user variable WEBSERVER_ROOT and had to create one
I had PATH's value as
C:\Inetpub\tpp-bin;C:\Program Files\Perl\site\bin;C:\Program Files\Perl
\bin;C:\Xcalibur\system\programs;C:\Program Files\Thermo\Foundation;C:
\cygwin\usr\X11R6\bin;C:\cygwin\bin;C:\Perl\site\bin;C:\Perl\bin;J:
\oracle\ora92\bin;C:\Program Files\Oracle\jre\1.1.8\bin;C:\Perl\bin;
%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;C:
\Program Files\Intel\DMIX;C:\cygwin\usr\X11R6\bin;C:\cygwin\bin;C:
\Program Files\QuickTime\QTSystem\;C:\strawberry\c\bin;C:\strawberry
\perl\site\bin;C:\strawberry\perl\bin
so I changed it to yours, and rebooted the computer, which still did
not solve the problem.
d) Heres my snippet of "httpd.conf" in Apache
#
# Begin settings for the Trans Proteomic Pipeline
#
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
#
Thanks in advance for your advices.
Regards,
Chris
On Oct 20, 5:39 pm, Vishal Swaroop <[email protected]> wrote:
> Hi Chris,
>
> Good to know that it worked..
>
> I am not sure about step7 (please send me the url you are referring).
>
> I am sure there were lot of things dependent on OS.. may be try this...
> restart after if changing variables as I think System variable change
> requires restart but not user variable change... so just re-start.. :)
>
> a) I assume you have default data directory i.e. "C:" Check if you have
> "C:\tmp", if not then create it.
> b) Which browser you are using, I am using IE8 and it works fine.
> c) Right click : "My Computer">Properties>Advanced Tab> Environment
> variables
> Check User variable :
> Variable name : WEBSERVER_ROOT
> Variable value : C:\Inetpub\wwwroot
>
> Check System Variables :
> Variable name "PATH" should have
> C:\Inetpub\tpp-bin;C:\Perl\site\bin;C:\Perl\bin;
>
> d) Here is snippet of Apache "httpd.conf" file which you can compare..
>
> #
> # Begin settings for the Trans Proteomic Pipeline
> #
>
> # Add 5-hour timeout
> Timeout 18000
>
> AddType text/html .shtml
> AddHandler server-parsed .shtml
>
> SetEnv WEBSERVER_ROOT C:/Inetpub/wwwroot
> SetEnv WEBSERVER_URLhttp://localhost:81
>
> 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
> </Directory>
>
> Alias /ISB "C:/Inetpub/wwwroot/ISB"
> Alias /isb "C:/Inetpub/wwwroot/ISB"
> <Directory "C:/Inetpub/wwwroot/ISB">
> Options Indexes MultiViews Includes ExecCGI
> AllowOverride None
> Order allow,deny
> Allow from all
>
> AddType text/html .shtml
> AddHandler server-parsed .shtml
> PassEnv WEBSERVER_ROOT
> </Directory>
>
>
>
>
>
>
>
> On Thu, Oct 20, 2011 at 7:02 PM, Chris L <[email protected]> wrote:
> > Hi all,
> > I am still encountering problem with tutorial step 6 which I am
> > ignoring for now.
> > In step 7, I am not able to open pepXML viewer for my interact.pep.xml
> > and here's the screen I get when trying to open it:
> >http://flic.kr/p/axzsk8
> > Any tip appreciated. Thanks again.
>
> > Regards,
> > Chris
>
> > On Oct 20, 3:39 pm, Chris L <[email protected]> wrote:
> > > Changing the domain to localhost:8080 solved the problem.
> > > Thanks a lot Vishal.
>
> > > Regards,
> > > Chris
>
> > > On Oct 19, 6:55 am, Vishal Swaroop <[email protected]> wrote:
>
> > > > Which browser you are using, firefox ?, try using IE or other
>
> > > > First check if Apache is configured correctly, tryhttp://localhost, you
> > > > should see "It works!" message on browser, if you have port other than
> > > > default (80) then usehttp://localhost:<your port>
>
> > > > Then try http://<localhost>:<port>/tpp-bin/tpp_gui.pl, if you have not
> > > > changed the port then it should be
> >http://localhost/tpp-bin/tpp_gui.pl
>
> > > > ..\Apache...\conf\httpd.conf should have information of host and port.
>
> > > > Hope this helps..
>
> > > > On Tue, Oct 18, 2011 at 7:46 PM, Chris L <[email protected]> wrote:
> > > > > localhost/tpp-bin/tpp_gui.pl
>
> > > > > The web browser changes it towww.localhost.comautomatically.
>
> > > > > Chris
>
> > > > > On Oct 18, 4:44 pm, Chris L <[email protected]> wrote:
> > > > > > No, I havehttp://www.localhost.com/tpp-bin/tpp_gui.pl
> > > > > > Formatting of my post caused the confusion
>
> > > > > > Regards,
> > > > > > Chris
>
> > > > > > On Oct 18, 4:19 pm, "Vensel, William" <[email protected]
>
> > > > > > wrote:
>
> > > > > > > Hi Chris,
>
> > > > > > > Is there a blank space in yur web address? // Local vs //local
>
> > > > > > > Bill
>
> > > > > > > -----Original Message-----
> > > > > > > From: [email protected] [mailto:
> > > > > [email protected]] On Behalf Of Chris L
> > > > > > > Sent: Tuesday, October 18, 2011 3:28 PM
> > > > > > > To: spctools-discuss
> > > > > > > Subject: [spctools-discuss] Re: TPP Demo 2009
>
> > > > > > > Hi Luis and all,
>
> > > > > > > I have uninstalled Microsoft IIS from the windows component
> > (running
> > > > > > > windows XP) and re-installed TPP v4.5 with the default Apache
> > > > > > > webserver. Now the problem is when I try to access the GUI
> > (http://
> > > > > > > localhost/tpp-bin/tpp_gui.pl), I get a blank page. Refreshing
> > the page
> > > > > > > and rebooting doesn't help. Any tips and advice appreciated.
>
> > > > > > > Sorry for all the miniscule questions and thanks again for being
> > > > > > > patient.
>
> > > > > > > Regards,
> > > > > > > Chris
>
> > > > > > > On Oct 14, 4:11 pm, Luis Mendoza <
> > [email protected]>
> > > > > > > wrote:
> > > > > > > > Hello Chris,
> > > > > > > > From the "timeout" error screenshot, it seems that you are
> > using the
> > > > > IIS
> > > > > > > > server. The TPP does not support this web server; instead we
> > > > > recommend that
> > > > > > > > you install and run the Apache web server -- which is bundled
> > and
> > > > > installed
> > > > > > > > with the TPP (provided you check the default boxes in the
> > install
> > > > > wizard).
>
> > > > > > > > Hope this helps,
> > > > > > > > --Luis
>
> > > > > > > > On Fri, Oct 14, 2011 at 4:04 PM, Chris L <[email protected]>
> > wrote:
> > > > > > > > > Dear all,
>
> > > > > > > > > I am experimenting with the TPP demo 2009 (http://
> > > > > > > > > tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009)
> > and
> > > > > > > > > encountered two problems.
>
> > > > > > > > > First, for step 6: Validation of Peptide-Spectrum assignments
> > with
> > > > > > > > > PeptideProphet, I can never get past the Run XInteract step.
> > My
> > > > > > > > > command does not finish running even after over a day!
> > (screen:
> > > > > > > > >http://flic.kr/p/avNB4R)
>
> > > > > > > > > Second, when I am trying step 7: Visualize LC-MS/MS data
> > using
> > > > > Pep3D.
> > > > > > > > > My browser tab shows "Connecting..." and a blank page that
> > does not
> > > > > > > > > load and eventually turns into a CGI error page (screen:
> > > > > > > > >http://flic.kr/p/avNAXk)
>
> > > > > > > > > Any suggestion appreciated. Thank you.
>
> > > > > > > > > Regards,
> > > > > > > > > Chris
>
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