Thanks a lot Charles for your time. To some extent I am to configure mapped network drive but still there are few issues with Apache/ Cgi.
- Thanks for sharing httpd.conf, I believe *D:* is your local shared drive ? After clean installatin of "TPP_Setup_v4_3_JETSTREAM_rev_1", "ActivePerl-5.8.9.827-MSWin32-x86-291969" "Apache 2.2.14" on WinXP ver2002 sp2, I am somehow able to write data files to network drive (it does not gets stuck on PepXmlViewer) *Issue:* a) On each click and when I clicking "Run XInteract" button blank command window appears and closes. b) I can start apache from command prompt but not from Apache monitor after mapping network drive. c) When I try to browse the above url, IE 6 hangs and I get the message At the top of the page I get the error: Messages "Unable to access xml file via webserver, so cannot check xml file for changes () Check webserver configuration if desired. (URL: undefined)" I only changed Alias for ISB, Alias for /tpp-bin is still "C:/Inetpub/tpp-bin": SetEnv WEBSERVER_ROOT Z:/Inetpub/wwwroot Alias /ISB "Z:/Inetpub/wwwroot/ISB" <Directory "Z:/Inetpub/wwwroot/ISB"> On Tue, Mar 16, 2010 at 12:23 PM, Charles <[email protected]> wrote: > I just followed the instructions more or less from > http://frank.neatstep.com/node/11 > with the directory change from C:\ to D:\. > > I've uploaded my httpd.conf file in the Files section. > > Hope this helps, > Charles > > On Mar 16, 9:11 am, ChargedPeptide <[email protected]> wrote: > > Hi, just wanted to let you know that pepXMLCGIViewer seems to hang > > when processing reuslts where > > > > "X:/Inetpub/wwwroot/ISB/data/SAN/iclData/server/Test_Executer/research/ > > 022710_G0311_P01129 > > _PQD_01 (MASCOT)"... > > => Total of 0 hits. > > Happens, as in your case, regardless of me not having modified the > > data directory.. > > You should probably try a different set of data for double checking > > this, where the final hits are >0. > > > > On Mar 15, 3:10 am, Vishal Swaroop <[email protected]> wrote: > > > > > > > > > Hi Charles, > > > > > I tried everything... but it is possible that I am missing something > very > > > small, should I also change tpp-bin path in httpd.conf. > > > > > It will be of great help if you can send your httpd.conf and tppgui.pl > > > > > It works for other files,but hangs on PepXMLViewer.cgi while creating > > > .xml.index file.. > > > > > Pls help. > > > > > Regards > > > Val > > > > > On Sat, Mar 13, 2010 at 8:48 PM, Charles <[email protected]> > wrote: > > > > 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 > > > > > > 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 > > > > ... > > > > read more ยป > > -- > 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. 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.
