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_URL http://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_Carbamidomethyl_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/022710_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/022710_G0311_P01129_PQD_01.pep.xml" -L"20"" file 1: x:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/022710_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 to http://localhost/ISB/data/SAN/iclData/server/Test_Executer/research/Test_interact.shtml 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/022710_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:_Installing_on_Ubuntu_9.04 > > > . > > > 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 to http://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 > > > #SetEnv WEBSERVER_ROOT /usr/local/apps/tpp > > > SetEnv WEBSERVER_ROOT /var/www > > > > > > > > > # Access logs > > > <IfModule log_config_module> > > > # Directives defining formatting of access log output > > > LogFormat "%h %l %u %t \"%r\" %>s %b \"%{Referer}i\" > > > \"%{User-Agent}i > > > \"" combined > > > LogFormat "%h %l %u %t \"%r\" %>s %b" common > > > > > > <IfModule logio_module> > > > # You need to enable mod_logio.c to use %I and > %O > > > LogFormat "%h %l %u %t \"%r\" %>s %b > \"%{Referer}i\" > > > \"%{User- > > > Agent}i\" %I %O" combinedio > > > </IfModule> > > > CustomLog /var/log/tpp/tpp_access_log common > > > </IfModule> > > > > > > <Directory /> > > > Options FollowSymLinks > > > AllowOverride None > > > </Directory> > > > #<Directory /usr/local/apps/tpp/> > > > <Directory /var/www/> > > > Options Indexes FollowSymLinks MultiViews > > > AllowOverride All > > > Order allow,deny > > > allow from all > > > </Directory> > > > > > > ScriptAlias /cgi-bin/ /usr/lib/cgi-bin/ > > > <Directory "/usr/lib/cgi-bin"> > > > AllowOverride None > > > Options +ExecCGI -MultiViews +SymLinksIfOwnerMatch > > > Order allow,deny > > > Allow from all > > > </Directory> > > > > > > ErrorLog /var/log/apache2/error.log > > > > > > # Possible values include: debug, info, notice, warn, error, > crit, > > > # alert, emerg. > > > LogLevel warn > > > > > > CustomLog /var/log/apache2/access.log combined > > > > > > # directory to store data for web browser viewing > > > ScriptAlias /tpp/data "/usr/local/apps/tpp/data" > > > <Directory "/usr/local/apps/tpp/data"> > > > AllowOverride None > > > Options Indexes FollowSymLinks Includes > > > Order allow,deny > > > Allow from all > > > </Directory> > > > > > > # directory for tpp's html resources (css, js, images, etc) > > > ScriptAlias /tpp/html "/usr/local/apps/tpp/html" > > > <Directory "/usr/local/apps/tpp/html"> > > > AllowOverride None > > > Options Includes Indexes FollowSymLinks MultiViews > > > Order allow,deny > > > Allow from all > > > </Directory> > > > > > > # directory for tpp's schema resources > > > <Directory "/usr/local/apps/tpp/schema"> > > > AllowOverride None > > > Options Includes Indexes FollowSymLinks MultiViews > > > Order allow,deny > > > Allow from all > > > </Directory> > > > > > > # directory for tpp's executable files > > > ScriptAlias /tpp/cgi-bin "/usr/local/apps/tpp/cgi-bin" > > > <Directory "/usr/local/apps/tpp/cgi-bin"> > > > #AllowOverride AuthConfig Limit > > > AllowOverride All > > > Options Indexes FollowSymLinks MultiViews ExecCGI > +Includes > > > AddHandler default-handler .jpg .png .css .ico .gif > > > AddHandler cgi-script .cgi .pl > > > Order allow,deny > > > Allow from all > > > SetEnv WEBSERVER_ROOT /usr/local/apps > > > #SetEnv WEBSERVER_ROOT /var/www > > > </Directory> > > > </VirtualHost> > > > > > > -------------------------- END HTTPD.CONF > > > -------------------------------- > > > > > > -- > > > 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]<spctools-discuss%[email protected]> > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > > > > . > > > For more options, visit this group at > > > http://groups.google.com/group/spctools-discuss?hl=en. > > > > > > > > -- > 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]<spctools-discuss%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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