The easiest fix I have found for this problem is not the most elegant,
but it works:
I have my data on my D: drive. I created an exact clone of everything
that is under C:/Inetpub on D:, including all the files in the tpp-bin
folder.
So on my D drive, I have an Inetpub folder that contains a wwwroot
folder as well as a copy of the complete tpp-bin folder (Having a copy
of tpp-bin is a bit of overkill, and most of the files don't need to
be in both locations, but it's easier to have 200 MB of duplicate
files than to parse out which files are necessary to have in the data
drive).
I keep my data in D:/Inetpub/wwwroot/data/. Doing it this way (having
a clone directory) makes it much easier when editing the tpp_gui.pl
and creating the aliases. Mine looks like this:
my $www_root = readconfig('www_root',"d:/Inetpub/wwwroot/"); #
full path to web server root
my $data_dir = readconfig('data_dir',"${www_root}ISB/
data/"); # full path to data directory top-level
All you have to do is change every incidence of C to D (or in your
case, G).
On Aug 18, 5:31 am, ZeiserMHH <[email protected]> wrote:
> 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"
>
> > > > ===============================- Hide quoted text -
>
> - Show quoted text -
--~--~---------~--~----~------------~-------~--~----~
You received this message because you are subscribed to the Google Groups
"spctools-discuss" group.
To post to this group, send email to [email protected]
To unsubscribe from this group, send email to
[email protected]
For more options, visit this group at
http://groups.google.com/group/spctools-discuss?hl=en
-~----------~----~----~----~------~----~------~--~---
