Hi,
Try point (1) it should solve pepxmlviewer.cgi hanging issue (if your other
permissions are OK):
Let me know ?
1) Do you have "tmp" directory under "d:" root ? if not create it manually
and try again.
I am using d: drive as data-drive and tpp installation is under "C:" drive.
My www_root is set to "d:/Inetpub/wwwroot/'
2) Check these also:
a) D drive should have this structure
d:\Inetpub\tpp-bin
d:\Inetpub\wwwroot
d:\tmp
b) C:\Inetpub\tpp-bin\tpp_gui.pl
Change my $www_root = readconfig('www_root',"d:/Inetpub/wwwroot/"); #
full path to web server root
c) Your command is picking up "c:\wwwroot" from WEBSERVER_ROOT (environment
variable) set during installation, check if it is under User or system
variable, change it accordingly (I think if it is under System variable then
you need to reboot).
d) My apache httpd.conf looks like this :
#
# Begin settings for the Trans Proteomic Pipeline
#
# Add 5-hour timeout
Timeout 18000
AddType text/html .shtml
AddHandler server-parsed .shtml
SetEnv WEBSERVER_ROOT D:/Inetpub/wwwroot
SetEnv WEBSERVER_URL http://<serverName>: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 "D:/Inetpub/wwwroot/ISB"
Alias /isb "D:/Inetpub/wwwroot/ISB"
<Directory "D:/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 Wed, Sep 1, 2010 at 9:45 AM, walmsls <[email protected]> wrote:
> Hi All.
> I recently re-installed TPP to new hardware, and would like my data
> drive set to d: for wwwroot.
>
> Upon making all the suggested changes (http.conf, webserver_root,
> tpp_gui.pl) the software is hanging at pepxmlviewer.cgi during
> xinteract. Interestingly, the webserver root environment variable is
> not passed to the command (last line). The command block that has been
> giving me this error follows, with the final command showing the
> reference to c:\wwwroot instead of the intended d:\wwwroot. Additional
> errors include webserver-root errors peppered throughout the following
> log. Is there anything additional I may have missed to get this
> working?
> Thanks!!!
>
>
>
> # Commands for session VMEAWVVHD on Wed Sep 1 07:08:15 2010
> # BEGIN COMMAND BLOCK
> ###### BEGIN Command Execution ######
> [Wed Sep 1 07:08:15 2010] EXECUTING: run_in d:/Inetpub/wwwroot/ISB/
> data/test; c:\Inetpub\tpp-bin\xinteract -Ninteract.pep.xml -p0.05 -l7
> -O d:/Inetpub/wwwroot/ISB/data/test/BBMV_ID1.tandem.pep.xml
> OUTPUT:
>
> c:\Inetpub\tpp-bin\xinteract (TPP v4.4 VUVUZELA rev 0, Build
> 201008161532 (MinGW))
>
> running: "C:/Inetpub/tpp-bin/InteractParser "interact.pep.xml" "d:/
> Inetpub/wwwroot/ISB/data/test/BBMV_ID1.tandem.pep.xml" -L"7""
> warning: xsl file d:/inetpub/wwwroot/ISB/data/test/interact.pep.xsl
> must begin with the WEBSERVER_ROOT path for use with a webserver.
> file 1: d:/Inetpub/wwwroot/ISB/data/test/BBMV_ID1.tandem.pep.xml
> processed altogether 1894 results
> problem (ph8): d:/Inetpub/wwwroot/ISB/data/test/interact.pep.xml is
> not mounted under webserver root: c:/Inetpub/wwwroot/
> command completed in 1 sec
>
> running: "C:/Inetpub/tpp-bin/PeptideProphetParser "interact.pep.xml"
> MINPROB=0.05"
> (X! Tandem (k-score))
> init with X! Tandem (k-score) trypsin
> MS Instrument info: Manufacturer: Agilent, Model: AGILENT TOF,
> Ionization: MS_CHIP, Analyzer: QTOF, Detector: unknown
>
> PeptideProphet (TPP v4.4 VUVUZELA rev 0, Build 201008161532 (MinGW))
> akel...@isb
> read in 0 1+, 1843 2+, 20 3+, 10 4+, 0 5+, 0 6+, and 0 7+ spectra.
> Initialising statistical models ...
> negmean = 0.0533258
> negmean = -0.638858
> negmean = -0.650452
> negmean = -0.0954922
> negmean = -0.2
> negmean = -0.2
> negmean = -0.2
> Iterations: .........10.........20.
> model complete after 22 iterations
> command completed in 0 sec
>
> running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i interact.pep.xml"
> Analyzing interact.pep.xml ...
> Parsing search results "d:/Inetpub/wwwroot/ISB/data/test/BBMV_ID1 (X!
> Tandem (k-score))"...
> => Total of 1293 hits.
> command completed in 1 sec
>
> running: "C:/Inetpub/tpp-bin/DatabaseParser "interact.pep.xml""
> command completed in 1 sec
>
> running: "C:/Inetpub/tpp-bin/RefreshParser "interact.pep.xml" "d:/
> Inetpub/wwwroot/ISB/data/dbase/BMV_Temporal.fasta""
> - Searching the tree...
> - Linking duplicate entries... - Printing results...
>
> - Building Commentz-Walter keyword tree...command completed in 1
> sec
>
> running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I d:/Inetpub/
> wwwroot/ISB/data/test/interact.pep.xml"
>
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