data folder:different drive: problem

[ZeiserMHH]

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_Petunia#How_to_change_the_location_of_the_data_files

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)) AKeller@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"

===============================

[Kristian]

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 <zeiser.johan...@mh-hannover.de> 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...

[ZeiserMHH]

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

[ZeiserMHH]

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?

[Kristian]

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).

> > > > ===============================- Hide quoted text -
>
> - Show quoted text -

[Brian Pratt]

Actually for these kind of customizations you should edit the
tpp_gui_config.pl file instead of hacking the tpp_gui.pl file. That way
they won't get stomped when you do a software update.

In your case you'd want to add these lines, somewhere in the middle of the
tpp_gui_config.pl file after the line "# SET TPP_GUI DEFAULTS HERE":

'base_dir' => 'd:\\Inetpub\\tpp-bin\\',
'www_root' => 'd:/Inetpub/wwwroot/',

Hope this helps,

Brian

[ZeiserMHH]

Hello Brian, Hello Kristian,

thank you for your help.

i tried changing drive letters and adding installations on c:, but it
just did not work. i got error messages that files in a tmp-folder
could not be found, because the location is missing, when i wanted to
start a x!tandem database search

i came to the conclusion, that it might be best to reinstall tpp and
transfer the data i want to process from its drive to c:, so after i
extracted all information i want i would move the processed data back
to its original location.
so, after installing tpp on c and moving some mzXML file in the data
folder i tried to run a x!tandem database search. it seems to work,
but there is a repeating popping up of a command-line window which
really kills my nerves :)

do you have any idea what could be the cause for this and how i could
stop it?

thanks again,

johannes

[Brian Pratt]

That does sound annoying - can you read its contents?

[pth]

In my opnion, don't change any TPP settings or you'll see many bugs...

Just try to create a symbol link to c:/Inetpub/wwwroot/ISB/data .


Step 1. download junction tool from http://download.sysinternals.com/Files/Junction.zip
.

Step 2. extract junction.zip to C:\WINDOWS\system32 .

Step 3. move all data from c:/Inetpub/wwwroot/ISB/data to your new
data direction (ie. G:/data) and delete c:/Inetpub/wwwroot/ISB/data
directory.

Step 4. open command prompt and input " junction C:\Inetpub\wwwroot\ISB
\data G:\data.

Step 5. edit C:\AppServ\Apache2.2\conf\httpd.conf, add
"FollowSymlinks" between <Directory "C:/Inetpub/wwwroot"> like below.

<Directory "C:/Inetpub/wwwroot">
Options Indexes MultiViews Includes FollowSymlinks

AllowOverride None
Order allow,deny
Allow from all

AddType text/html .shtml
AddHandler server-parsed .shtml

PassEnv WEBSERVER_ROOT
PassEnv WEBSERVER_TMP
</Directory>

Step 6. restart apache


That's all.

[ZeiserMHH]

hi pth, hi brian,

i was not able to read the command-line pop-up and finally decided to
deinstall tpp 4.3 and reinstall 4.2, after which everything worked
fine again (except for not having drive g: as data-storage)

using the junction tool sounds very promising, i definitely will try
that.

thanks a lot,

johannes