Hey Val, so that also happened to me when I tried to change ONLY the data location as you have. the xinteract got stuck somewhere as well, probably the same place you got stuck. So just change all the Directory tags to point to //server/Inetpub/ .. etc. And again make sure you leave a copy of the tpp-bin on the C: since it seems like some of the paths are hardcoded into the executables.
Charles On Mar 12, 10:23 am, Vishal Swaroop <[email protected]> wrote: > Thanks for replying Charles... I tried the following, but it gets stuck on > running "PepXMLViewer.cgi" > > If any one can help on this, I will be very thankful.... > > Issue : > When I run XInteract even from command prompt all processes like > "InteractParser, PeptideProphetParser, ProphetModels, DatabaseParser, > RefreshParser" runs fine BUT it gets stuck on running "PepXMLViewer.cgi" > > Brief details : > a) I have exact copy of Inetpub from my c drive to mapped network drive. > > b) Consider my mapped drive is X: and I can see > X:\Inetpub\wwwroot and X:\Inetpub\tpp-bin > > c) I can also browse using \\server\Inetpub\ <file://server/Inetpub/> > d) My httpd.conf looks like this i.e. changed data drive to > *Alias /ISB "//server/Inetpub/wwwroot/ISB" > <Directory "//server/Inetpub/wwwroot/ISB">* > --------------------------------------------------------------------------- > -------------- > AddType text/html .shtml > AddHandler server-parsed .shtml > SetEnv WEBSERVER_ROOT X:/Inetpub/wwwroot > SetEnv WEBSERVER_URLhttp://localhost:80<http://localhost/> > *Alias /ISB "//server/Inetpub/wwwroot/ISB" > <Directory "//server/Inetpub/wwwroot/ISB"> > * AllowOverride None > Options Includes Indexes FollowSymLinks MultiViews > Order allow,deny > Allow from all > AddType text/html .shtml > AddHandler server-parsed .shtml > </Directory> > 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 > PassEnv WEBSERVER_TMP > </Directory> > Alias /schema "C:/Inetpub/wwwroot/schema" > <Directory "C:/Inetpub/wwwroot"> > Options Indexes MultiViews Includes > AllowOverride None > Order allow,deny > Allow from all > AddType text/html .shtml > AddHandler server-parsed .shtml > PassEnv WEBSERVER_ROOT > PassEnv WEBSERVER_TMP > </Directory> > --------------------------------------------------------------------------- > -------------- > > e) changed "www_root" in tpp_gui.pl > my $base_dir = readconfig('base_dir',"c:\\Inetpub\\tpp-bin\\"); # full > path to this file > my $www_root = readconfig('www_root',"x:/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 > > f) When I run XInteract even from command prompt all processes like > "InteractParser, PeptideProphetParser, ProphetModels, DatabaseParser, > RefreshParser" runs fine BUT it gets stuck on running "PepXMLViewer.cgi" > > *"running: "X:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/Test_ > interact.xml"" > * > > This is the out-put on command window.... > --------------------------------------------------------------------------- > -------------------------- > X:\Inetpub\wwwroot\ISB\data\SAN\aTPPiclData\server\Test_Executer\iTRAQ_Carb > amidomethyl_PQD_research>run_in > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research; > x:\Inetpub\tpp-bin\xinteract -NTest_interact.xml -p0.000 -l20 -Op -dREV > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/02271 > 0_G0311_P01129_PQD_01.pep.xml > x:\Inetpub\tpp-bin\xinteract (TPP v4.3 JETSTREAM rev 1, Build 200909091257 > (MinGW)) > running: "C:/Inetpub/tpp-bin/InteractParser "Test_interact.xml" > "x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/0227 > 10_G0311_P01129_PQD_01.pep.xml" > -L"20"" file 1: > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/02271 > 0_G0311_P01129_PQD_01.pep.xml > processed altogether 1445 results > > results written to file > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/Test_ > interact.xml > direct your browser > tohttp://localhost/ISB/data/SAN/iclData/server/Test_Executer/research/T... > > command completed in 33 sec > running: "C:/Inetpub/tpp-bin/PeptideProphetParser "Test_interact.xml" > MINPROB=0.000 DECOY=REV" > Using Decoy Label "REV". > (MASCOT) (minprob 0) > results for charge 1: 0 id tot and 0 adj scores > results for charge 2: 1152 id tot and 213 adj scores > results for charge 2: 11.1517 adj_ion_mean and 18.5814 adj_ion_hom mean > 39.2id mean0.937465 correlation (r) > 2+ ion - id = 1.15829*(ion - hom) + -10.371 with error = 6.88606 > mean ion - id: 11.1517, mean ion - hom: 18.5814 > results for charge 3: 274 id tot and 63 adj scores > results for charge 3: 0.766935 adj_ion_mean and 14.5513 adj_ion_hom mean > 39.8226id mean0.951025 correlation (r) > 3+ ion - id = 1.20602*(ion - hom) + -16.7822 with error = 4.3439 > mean ion - id: 0.766935, mean ion - hom: 14.5513 > results for charge 4: 17 id tot and 0 adj scores > results for charge 5: 2 id tot and 0 adj scores > results for charge 6: 0 id tot and 0 adj scores > results for charge 6: -0 adj_ion_mean and -0 adj_ion_hom mean 0id meannan > correlation (r) > results for charge 7: 0 id tot and 0 adj scores > init with MASCOT trypsin > MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ Orbitrap XL, > Ionization: ESI, Analyzer: Ion Trap, Detector: EMT > PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909091257 (MinGW)) > akel...@isb > read in 0 1+, 4 2+, 11 3+, 2 4+, 2 5+, 0 6+, and 0 7+ spectra. > Initialising statistical models ... > Iterations: .........10.........20 > WARNING: Mixture model quality test failed for charge (2+). > WARNING: Mixture model quality test failed for charge (3+). > WARNING: Mixture model quality test failed for charge (4+). > WARNING: Mixture model quality test failed for charge (5+). > model complete after 21 iterations > command completed in 19 sec > running: "C:/Inetpub/tpp-bin/ProphetModels.pl -i Test_interact.xml" > Analyzing Test_interact.xml ... > Parsing search results > "X:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/0227 > 10_G0311_P01129 > _PQD_01 (MASCOT)"... > => Total of 0 hits. > command completed in 3 sec > running: "C:/Inetpub/tpp-bin/DatabaseParser "Test_interact.xml"" > command completed in 1 sec > running: "C:/Inetpub/tpp-bin/RefreshParser "Test_interact.xml" > "X:/Inetpub/wwwroot/ISB/data/dataDrive/FASTA/IPI/HUMAN/IPI_HUMAN.fasta"" > - Building Commentz-Walter keyword tree... - Searching the tree... > - Linking duplicate entries... - Printing results... > command completed in 59 sec > running: "X:/Inetpub/wwwroot/../tpp-bin/PepXMLViewer.cgi -I > x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/Test_ > interact.xml" > ....gets stuck here forever > --------------------------------------------------------------------------- > -------------------------- > > Regards > Val > > > > On Thu, Mar 11, 2010 at 8:27 PM, Charles <[email protected]> wrote: > > Hi Val, > > > Sorry for the generic description, I just wanted to keep it short. > > But yes, D is just a partition on my local drive. I had a similar > > situation to you when I just tried changing the C:/Inetpub/wwwroot/ISB/ > > data to D:/data or something. So if it's not going to be a hassle, > > just copy the entire directory tree from C:/Inetpub to \\network > > \Inetpub and make the appropriate changes in the WWWROOT and PATH to > > reflect the change. > > > I also found that you have to keep /tpp-bin in the default location on > > the C: because it seems like some of programs (xinteract for one) have > > the C:\Inetpub\tpp-bin path hard coded into the binary. > > > Hope this helps, > > Charles > > > Vishal Swaroop wrote: > > > Hi Charles, > > > > For windows, is D drive local on your machine? > > > > I am trying to right data to mapped network drive, when I run XInteract > > from > > > GUI, it hangs on PepXMLViewer.cgi forever, do you have any idea. > > > > Regards > > > Val > > > > On Thu, Mar 11, 2010 at 1:40 PM, Charles <[email protected]> > > wrote: > > > > > Hello, > > > > > I've searched around for this topic and found articles on how to > > > > relocate the entire directory structure in windows (which I've done > > > > and it works out) by changing C:\ to D:\ in the apache2/conf/ > > > > httpd.conf file, copying the entire folder hierarchy to D:\ and > > > > changing the WEBSERVER_ROOT and PATH to D:\. I wanted to do something > > > > similar in Ubuntu 9.10 (and other linux distros) so I installed the > > > > TPP v4.3 rev 1 following the instructions provided by > > >http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.2.1:_Insta... > > > > . > > > > All the binaries/scrips I want to use run fine, namely tandem.exe, > > > > Tandem2XML, and xinteract (I prefer to use the command line instead of > > > > the gui). The only issue is viewing the resultant data files through > > > > the browser. Below, I've included the httpd.conf file (as shown in > > > > the installation tutorial). > > > > > The first problem is that while the tpp_gui.pl script opens in the > > > > browser (http://localhost/tpp/cgi-bin/tpp_gui.pl), I get a "403 > > > > Forbidden, You don't have permission to access /tpp/data/ on this > > > > server" when I navigate tohttp://localhost/tpp/data. This occurs > > > > even if I give the /tpp/data directory read/write permission and even > > > > change owner to the user. > > > > > The second is, I would like to analyze my data in another directory, > > > > let's say /home/charles/data while keeping the binaries/scripts in > > > > the /usr/local/apps/tpp directory. I can only think of the following > > > > changes: > > > > > ScriptAlias /tpp/data "/usr/local/apps/tpp/data" ---> > > ScriptAlias / > > > > tpp/data "/home/charles/data" > > > > <Directory "/usr/local/apps/tpp/data"> ---> <Directory > > > > "/home/charles/ > > > > data"> > > > > > However, I still get the 403 Forbidden error. Does anyone know of how > > > > to make this arrangement work? Also, if you know of any instances of > > > > hard-coded directory variables that I may need to change, especially > > > > in xinteract, it would be much appreciated. > > > > > Thanks, > > > > Charles > > > > > ------------------------ BEGIN HTTPD.CONF > > > > ------------------------------- > > > > > <VirtualHost *:80> > > > > > DocumentRoot /var/www > > ... > > read more » -- 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.
