Hi All, I thought of sharing my experience for making TPP - Apache to work with network drive.
Here is my finding for trouble shooting Apache to recognize network drive. a) Latest apache version available is 2.2.14 but apache does not start as a service, and if we start apache from command prompt, network drives are recognized but we use to get blank command windows pop-ups on each click of TPP application running on apache. Even default version of apache (2.2.8) during TPP installation behaves in the same manner. b) This post says that it worked until Apache v2.0.32 AND works on a Win2000 server : http://osdir.com/ml/apache.devel/2002-06/msg00180.html c)(i) I tried with Apache/1.3.41 (Win32), Active perl v 5.10.1, TPP_Setup_v4_3_JETSTREAM_rev_1 on WinXp sp2. I can start pache from services but network drives are not recognized. (ii) Nework drives are recognized if I start apache from command prompt (using apache -k start), and we don't get any blank command windows pop-ups on each click of TPP application, all processing works fine. d) When TPP is installed it creates "tmp" folder under root installation directory (default "C:/"), it looks like tpp needs "tmp" folder (though it can be empty) under root directory. Make sure to make "tmp" directory under new root. e) I also think that there is no need to copy tpp-bin folder (though I have not tested) under new root, copying only wwwroot should also work. I will try to configure latest release of Apache (2.2.15) and will send the findings. My httpd.cnf looks like this (where "B:/" is network mapped drive) # # Begin settings for the Trans Proteomic Pipeline # # Add 5-hour timeout Timeout 18000 AddType text/html .shtml AddHandler server-parsed .shtml #SetEnv WEBSERVER_ROOT C:/Inetpub/wwwroot SetEnv WEBSERVER_ROOT B:/Inetpub/wwwroot SetEnv WEBSERVER_URL http://localhost:81 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 </Directory> Alias /ISB "B:/Inetpub/wwwroot/ISB" Alias /isb "B:/Inetpub/wwwroot/ISB" <Directory "B:/Inetpub/wwwroot/ISB"> Options Indexes MultiViews Includes AllowOverride None Order allow,deny Allow from all AddType text/html .shtml AddHandler server-parsed .shtml PassEnv WEBSERVER_ROOT </Directory> On Wed, Mar 17, 2010 at 6:52 PM, Charles <charlesyoo...@gmail.com> wrote: > Oh, that looks like some extraneous addition from the website I > referenced. The directory doesn't even exist, so I just removed the > entire Directory block and xinteract ran fine. > > On Mar 16, 4:16 pm, Val <vishal....@gmail.com> wrote: > > Hi Charles, > > > > Quick Question : I can see reference to "D:/Inetpub/isb-bin" in your > > httpd.conf, I don't have this when I installed > > "TPP_Setup_v4_3_JETSTREAM_rev_1" > > > > Is it because of some older version of TPP. > > > > On Mar 16, 12:23 pm, Charles <charlesyoo...@gmail.com> wrote: > > > > > > > > > I just followed the instructions more or less fromhttp:// > 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 <malm.e...@gmail.com> 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 <vishal....@gmail.com> 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 <charlesyoo...@gmail.com> > 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 <vishal....@gmail.com> 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 cdriveto > mappednetworkdrive. > > > > > > > > > b) Consider my mappeddriveis 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 datadriveto > > > > > > > *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 > > > > ... > > > > 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 spctools-disc...@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com<spctools-discuss%2bunsubscr...@googlegroups.com> > . > 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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