just wanted to add, that i can access files in the tpp-bin folder via
my browser but cannot access the .pl file
however when is switch the line
(Alias /tpp-bin "G:/Inetpub/tpp-bin"
<Directory "G:/Inetpub/tpp-bin">
Options Indexes MultiViews Includes
AllowOverride None
Order allow,deny
Allow from all)
" AddHandler cgi-script .cgi .pl
ScriptInterpreterSource Registry
to
" AddType text/html .shtml
AddHandler server-parsed .shtml
( PassEnv WEBSERVER_ROOT
</Directory>)
i have access to the code of the tpp_gui.pl file, so there seems to be
a problem with running the perl script on the server for some reason?
On 18 Aug., 13:41, ZeiserMHH <[email protected]> wrote:
> Hi Kristian,
>
> thank you for your help. i changed the letter of the drive in the
> environment variables, but when i wanted to start the gui i just
> received a message that the access to the folder is denied.
>
> i have the following setup of programs and data at the moment:
>
> Perl / apache-Server on c:\
>
> MS-Data i want to process: G:\Data\ESI\
>
> tpp: G:\Inetpub\tpp-bin\
>
> wwwroot: G:\Inetpub\wwwroot\
>
> maybe there is any flaw in this setup already?
>
> if anyone could give me a hint about how to edit httpd.conf and
> tpp_gui.pl i would be really glad!
>
> thanks a lot in advance,
>
> johannes
>
> On 12 Aug., 18:06, Kristian <[email protected]> wrote:
>
> > From the start menu, go to Control Panel, System, Advanced,
> > Environment Variables.
>
> > Near the end of the list is a variable called WEBSERVER_ROOT whose
> > value is c:\Inetpub\wwwroot
>
> > Change the "c" to the new drive letter. RESTART YOUR MACHINE. That
> > should fix it.
>
> > This was an issue on the cygwin-based TPP as well, but the Wiki does
> > not have this info.
>
> > On Aug 11, 6:20 am, ZeiserMHH <[email protected]> wrote:
>
> > > hello,
>
> > > i moved my data-folder to another drive and changed the settings for
> > > the server root folder in tpp_gui.pl as well as in apache httpd.conf
> > > according to
>
> > >http://tools.proteomecenter.org/wiki/index.php?title=TPP:Using_Petuni...
>
> > > i can access the files in the new location and perform a database
> > > search with them. however, when i try running a peptide analysis with
> > > them i get several error messages regarding the new location and the
> > > command is not finished. instead pepxmlviewer.cgi runs at 100% cpu
> > > usage and seems not to come to an end.
> > > Is there any other file i need to edit except from tpp_gui.pl and
> > > httpd.conf?
>
> > > please also see below the output of the task with the error messages.
>
> > > Thank you for your help!
>
> > > best regards,
>
> > > Johannes
>
> > > ===============================
>
> > > # Commands for session 0F2NBY3WV on Tue Aug 11 14:41:29 2009
> > > # BEGIN COMMAND BLOCK
> > > ###### BEGIN Command Execution ######
> > > [Tue Aug 11 14:41:30 2009] EXECUTING: run_in G:/Daten/ESI/JZ/J090716/
> > > Z11.D; c:\Inetpub\tpp-bin\xinteract -NZ11.pep.xml -p0.05 -l7 -Op -X-
> > > m0.2-nK,6-nR,10 -A-lRK-F-r0.2-mR166.11K134.11 G:/Daten/ESI/JZ/J090716/
> > > Z11.D/Z11.tandem.pep.xml
> > > OUTPUT:
>
> > > c:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 0, Build
> > > 200908071234 (MinGW))
>
> > > running: "C:/Inetpub/tpp-bin/InteractParser "Z11.pep.xml" "G:/Daten/
> > > ESI/JZ/J090716/Z11.D/Z11.tandem.pep.xml" -L"7""
> > > warning: xsl file g:/daten/esi/jz/j090716/Z11.D/Z11.pep.xsl must begin
> > > with the WEBSERVER_ROOT path for use with a webserver.
> > > file 1: G:/Daten/ESI/JZ/J090716/Z11.D/Z11.tandem.pep.xml
> > > processed altogether 293 results
> > > problem (ph8): g:/Daten/ESI/JZ/J090716/Z11.D/Z11.pep.xml is not
> > > mounted under webserver root: c:/Inetpub/wwwroot/
> > > command completed in 0 sec
>
> > > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "Z11.pep.xml"
> > > MINPROB=0.05"
> > > (X! Tandem)
> > > init with X! Tandem trypsin
> > > MS Instrument info: Manufacturer: Bruker Daltonics, Model: esquire,
> > > Ionization: ESI, Analyzer: Quadrupole Ion Trap, Detector:
>
> > > PeptideProphet (TPP v4.3 JETSTREAM rev 0, Build 200908071234
> > > (MinGW)) akel...@isb
> > > read in 0 1+, 190 2+, 102 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra.
> > > Initialising statistical models ...
> > > negmean = 0.0533258
> > > negmean = 1
> > > negmean = -0.2
> > > negmean = -0.2
> > > negmean = -0.2
> > > negmean = -0.2
> > > negmean = -0.2
> > > Iterations: .........10.........20.
> > > WARNING: Mixture model quality test failed for charge (2+).
> > > WARNING: Mixture model quality test failed for charge (3+).
> > > model complete after 22 iterations
> > > command completed in 0 sec
>
> > > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i Z11.pep.xml"
> > > Analyzing Z11.pep.xml ...
> > > Parsing search results "G:/Daten/ESI/JZ/J090716/Z11.D/Z11 (X!
> > > Tandem)"...
> > > => Total of 0 hits.
> > > command completed in 1 sec
>
> > > running: "C:/Inetpub/tpp-bin/XPressPeptideParser "Z11.pep.xml" -m0.2 -
> > > nK,6 -nR,10"
> > > command completed in 1 sec
>
> > > running: "C:/Inetpub/tpp-bin/ASAPRatioPeptideParser "Z11.pep.xml" -lRK
> > > -F -r0.2 -mR166.11K134.11"
> > > WARNING: Found more than one variable mod on 'K'. Please make sure to
> > > specify a heavy mass for this residue.
> > > WARNING: Found more than one variable mod on 'R'. Please make sure to
> > > specify a heavy mass for this residue.
> > > command completed in 1 sec
>
> > > running: "C:/Inetpub/tpp-bin/DatabaseParser "Z11.pep.xml""
> > > command completed in 0 sec
>
> > > running: "C:/Inetpub/tpp-bin/RefreshParser "Z11.pep.xml" "G:/Daten/ESI/
> > > data/dbase/IPI/current/ipi.HUMAN.v3.62.fasta""
> > > - Searching the tree...
> > > - Linking duplicate entries... - Printing results...
>
> > > - Building Commentz-Walter keyword tree...command completed in 4
> > > sec
>
> > > running: "c:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I g:/Daten/
> > > ESI/JZ/J090716/Z11.D/Z11.pep.xml"
>
> > > ===============================
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