IPP installation

[spctoo...@googlemail.com]

I have installed ipp on my computer with windows xp, as the website
says that its a 30 days free. I have also installed apache 2.2 which
is working fine. But i am not able to open up the webinterface as it
says http 404 not found. i am not getting what must be going wrong.
tpp petunia is working fine on my system. please if you have some
suggestions.
thanks

[spctoo...@googlemail.com]

here is the path set under environment variables C:\Inetpub\ipp-bin;C:
\Perl\bin\;c:\Perl\bin;;C:\Program Files\Java\jre1.6.0_03\bin;C:
\Program Files\QuickTime\QTSystem\;C:\cygwin\usr\X11R6\bin;C:\cygwin
\bin
does this needs any changes, or does any other variable needs to be
changed or added.
please suggest.

On Feb 18, 12:38 pm, "spctools2...@googlemail.com"

[Brian Pratt]

I'd start by making sure you have the latest from the Insilicos website. It
sounds like you may be trying to run an older version? Also, if the web
page says 30 days free we need to fix that - it's just plain free now.

Thanks,

Brian Pratt

[research user]

I have downloaded  and installed the version ipp1-0-2.exe from http://www.insilicos.com/downloadIPP.html web  page. Please send me the link if there is another latest version available.

thanks

[Brian Pratt]

Oh my, thanks for letting me know about that.  It would appear that a very old version of that web page found its way back onto the website.  Please try the download again, you should get version 1.0.91 instead.

 

Thanks,

 

Brian Pratt

 

---

From: Insili...@googlegroups.com [mailto:Insili...@googlegroups.com] On Behalf Of research user
Sent: Monday, February 18, 2008 7:33 AM
To: Insili...@googlegroups.com
Subject: [IPP list] Re: IPP installation

 

I have downloaded  and installed the version ipp1-0-2.exe from http://www.insilicos.com/downloadIPP.html web  page. Please send me the link if there is another latest version available.

thanks

[research user]

Thanks, now I have installed the latest one and its working fine. I have started the analysis, I will come back to you if I have some queries.

Kanchan

[research user]

Why do I get this message when I try to openup the result file from peptide validation n pepxml viewer . i am able to open up other xml files in pepxml viewer

the message says

 

error with html display: XML parsing error: mismatched tag, at xml file line 5, column 2

 

I have attached the file here, if you are able to figure out the problem please let me know.it will help me to troubleshoot in future analysis.

 

thanks

 

Kanchan

[Bryan Prazen]

Kanchan,

I am unable to test this today, but I suspect that it might be that this file was made with the cygwin build of TPP.  Notice that all the paths start with /cygdrive/c.  If your using IPP, IPP is probably not able to find or open the files in the cygwin directory structure.  You could re-run the analysis or try to do a find and replace for the paths in this file.  I believe there is a tool under the 'Tools' tab of the IPP GUI that will check your pepXML results file for problems of this type and suggest fixes.

hope this helps,

Bryan 

[research user]

Dear Bryan,

Thanks for your mail, hopefuly you will be able to test the file today. Its a file generated from TPP, i tried to open it up in IPP and it did not open.

I have few  more questions now

I tried to run xtandem search with ipp

do i need to download x tandem to my computer, if so where it has to be saved, in C:/ or program files?

so for running xtandem from ipp one needs only input file, what about the taxonomy file?

 

I gave a try after and before downloading xtandem to my computer

the output i see is this, what does this error means

# Commands for session 33O1Z739K on Mon Mar  3 13:48:48 2008
# BEGIN COMMAND BLOCK
###### BEGIN Command Execution ######
[Mon Mar  3 13:48:48 2008] EXECUTING: c:\Inetpub\ipp-bin\run_in c:/Inetpub/wwwroot/ISB/kandata; tandem c:/Inetpub/wwwroot/ISB/kandata/F5tand_params.xml; c:\Inetpub\ipp-bin\msxml2other -dta F5.mzXML; c:\Inetpub\ipp-bin\Tandem2XML c:/Inetpub/wwwroot/ISB/kandata/F5tandem.xml c:/Inetpub/wwwroot/ISB/kandata/F5.xml 
OUTPUT:
The system cannot find message text for message number 0x2331 in the message file for Application.

command 'C:\Inetpub\ipp-bin\cmd.exe /C tandem c:\Inetpub\wwwroot\ISB\kandata\F5tand_params.xml' failed with code 1: Operation not permitted
Converting F5.mzXML to thermofinnigan dta
Failed to open input file 'c:\Inetpub\wwwroot\ISB\kandata\F5tandem.xml'.

command 'c:\Inetpub\ipp-bin\Tandem2XML.exe c:\Inetpub\wwwroot\ISB\kandata\F5tandem.xml c:\Inetpub\wwwroot\ISB\kandata\F5.xml' failed with code 1: Operation not permitted
END OUTPUT
RETURN CODE:256
###### End Command Execution ######
# All finished at Mon Mar  3 13:52:37 2008
# END COMMAND BLOCK

Please guide, what is it that I am doing wrong.

Also its not possible to open up a pepxml file generated by TPP in IPP.

Also do you have any clue why I am unable to view the file which i have send you in my last mail in tpp's pepxml viewer, aas the file shows some xml parsing error.

Please guide,

thanks for your help

Kanchan

[research user]

Dear Bryan,

Here I have one more query.

I have run a file in Mascot and got the output in pepxml format.

Now when I try to visualise this file with IPP it says

PepXML File: c:/Inetpub/wwwroot//ISB/kandata/tppresults/jm.xml

Database:	/home/matrix/site/sequence/NCBInr/current/NCBInr_20080221.fasta	Warning: Database is not in the expected location!
Directories for MS data:	raw_data_type=	Warning: mzXML file is not in the expected location!
Stylesheet:	Warning: No stylesheet references found	Warning: Stylesheet is not in the expected location!
Search data directory:	http://www.matrixscience.com/cgi/master_results.pl?file=../data/20080226/FtgAorHaS.dat	Warning: Search results are not in the expected location!

Errors were found in this pepXML file. This might prevent processing or viewing of these results

 

also I could not visualise it in TPP either, it shows the similar parsing error.

Definitely there is something which I am doing wrong.

Please guide.

kanchan

[Bryan Prazen]

Kanchan,

What you sent is the PepXML file info that I tried to describe earlier (I think I told you to look for it under the tools tab).  I do not believe that IPP will work with pepXML data directly from the free Mascot server.  

All of your problems appear to be related to the fact that IPP and TPP need more files than the pepXML file.  They need to be able to find the pepXML file, database file, MS data file, stylesheet file and search data file/directory.  The locations of the other files are coded in the pepXML file.  When you move files the system breaks.  In the example below, the pepXML file was made on the Mascot server.  This server did not know where the other files were located.  Try making the pepXML through IPP.

hope this helps,

bryan