That does sound annoying - can you read its contents? -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of ZeiserMHH Sent: Thursday, August 20, 2009 7:14 AM To: spctools-discuss Subject: [spctools-discuss] Re: data folder:different drive: problem
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 On 20 Aug., 02:02, "Brian Pratt" <[email protected]> wrote: > 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 > > -----Original Message----- > From: [email protected] > > [mailto:[email protected]] On Behalf Of Kristian > Sent: Wednesday, August 19, 2009 4:48 PM > To: spctools-discuss > Subject: [spctools-discuss] Re: data folder:different drive: problem > > 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. 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