I have configured environment similar to yours, I am not sure how LogMeln works... may be you can suggest.
Let me know from where you got this "demo folder" and c:/Inetpub/wwwroot/ISB/data/*demo2009/spectrast* I don't have it after I installed *"TPP_Setup_v4_5_RAPTURE_rev_0"* On Tue, Nov 1, 2011 at 5:33 PM, Chris L <linci%uci....@gtempaccount.com>wrote: > Hi Vishal, > I tried some of your methods above including changing Apache to the > newest version (v2.2.21), but none of them solved the problem. > I can give you remote access to this computer. What method do you use? > I have LogMeIn installed in this computer. We can schedule a time for > us to look at the computer together at your convenience. > Thanks a lot. > > Regards, > Chris > > On Nov 1, 2:03 pm, Chris L <linci%uci....@gtempaccount.com> wrote: > > a) I have ActivePerl v5.14.2 > > b) X-interact is still running from yesterday... here's the output so > > far > > # Commands for session 27HRKV59U on Mon Oct 31 11:25:08 2011 > > # BEGIN COMMAND BLOCK > > ###### BEGIN Command Execution ###### > > [Mon Oct 31 11:25:08 2011] EXECUTING: run_in c:/Inetpub/wwwroot/ISB/ > > data/demo2009/spectrast; c:\Inetpub\tpp-bin\tandem c:/Inetpub/wwwroot/ > > ISB/data/demo2009/spectrast/OR20080317_S_SILAC- > > LH_1-1_01.tandem.params > > OUTPUT: > > > > X! TANDEM 2010.10.01.1 (LabKey, Insilicos and ISB) > > > > Loading spectra ..... loaded. > > Spectra matching criteria = 9660 > > Pluggable scoring enabled. > > Starting threads .. started. > > Computing models: > > 1234567 > > waiting for 2. done. > > > > sequences modelled = 7 ks > > Model refinement: > > > > waiting for 2 done. > > > > Merging results: > > from 2.... > > > > Creating report: > > initial calculations ..... done. > > sorting ..... done. > > finding repeats ..... done. > > evaluating results ..... done. > > calculating expectations ..... done. > > writing results ..... done. > > > > Valid models = 2576 > > > > Regards, > > Chris > > > > On Oct 31, 5:51 pm, Vishal Swaroop <vishal....@gmail.com> wrote: > > > > > > > > > > > > > > > > > Apart from other queries in my last email... let me know this first.. > > > a) Perl version ?, from command prompt use this > > > perl -version > > > > > b) Please try running X-Interact and see if it is successful, > X-Interact > > > uses PepXMLViewe.cgi and we will come to know if it passes this. > > > > > Thanks > > > Vishal > > > > > On Mon, Oct 31, 2011 at 2:13 PM, Chris L < > linci%uci....@gtempaccount.com>wrote: > > > > > > Refresher: I am having problem opening interact.pep.xml with TPP at > > > > tutorial step 7: Visualize LC-MS/MS data using Pep3D. (http:// > > > > tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009) > > > > > > On Oct 31, 11:03 am, Chris L <linci%uci....@gtempaccount.com> wrote: > > > > > Update: I was able to do the test.cgi as described in this webpage > > > > > (http://www.perlmonks.org/?node_id=44536) with no problem. > > > > > > > Regards, > > > > > Chris > > > > > > > On Oct 31, 10:56 am, Chris L <linci%uci....@gtempaccount.com> > wrote: > > > > > > > > Hi Vishal and all, > > > > > > > > Here is my check_env.pl > > > > > > SCRIPT_NAME = /tpp-bin/check_env.pl > > > > > > SERVER_NAME = localhost > > > > > > SERVER_ADMIN = waynec...@gmail.com > > > > > > HTTP_ACCEPT_ENCODING = gzip, deflate > > > > > > HTTP_CONNECTION = keep-alive > > > > > > REQUEST_METHOD = GET > > > > > > SYSTEMROOT = C:\WINDOWS > > > > > > HTTP_ACCEPT = > text/html,application/xhtml+xml,application/xml;q=0.9,*/ > > > > > > *;q=0.8 > > > > > > SCRIPT_FILENAME = C:/Inetpub/tpp-bin/check_env.pl > > > > > > COMSPEC = C:\WINDOWS\system32\cmd.exe > > > > > > SERVER_SOFTWARE = Apache/2.2.8 (Win32) > > > > > > HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 > > > > > > WINDIR = C:\WINDOWS > > > > > > QUERY_STRING = > > > > > > REMOTE_PORT = 2368 > > > > > > PATHEXT = .COM;.EXE;.BAT;.CMD;.VBS;.VBE;.JS;.JSE;.WSF;.WSH > > > > > > HTTP_USER_AGENT = Mozilla/5.0 (Windows NT 5.1; rv:7.0.1) Gecko/ > > > > > > 20100101 Firefox/7.0.1 > > > > > > SERVER_PORT = 8080 > > > > > > SERVER_SIGNATURE = > > > > > > HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 > > > > > > REMOTE_ADDR = 127.0.0.1 > > > > > > WEBSERVER_ROOT = C:\Inetpub\wwwroot\ > > > > > > SERVER_PROTOCOL = HTTP/1.1 > > > > > > PATH = C:\Inetpub\tpp-bin;C:\Perl\site\bin;C:\Perl\bin > > > > > > REQUEST_URI = /tpp-bin/check_env.pl > > > > > > GATEWAY_INTERFACE = CGI/1.1 > > > > > > SERVER_ADDR = 127.0.0.1 > > > > > > DOCUMENT_ROOT = C:/Program Files/Apache Software > Foundation/Apache2.2/ > > > > > > htdocs > > > > > > WEBSERVER_TMP = C:\Inetpub\wwwroot\tmp > > > > > > HTTP_HOST = localhost:8080 > > > > > > > > Link to my httpd.conf and cmd_ log files (in a zip file): > > > >http://www.mediafire.com/?a2qn18wb8gc7lea > > > > > > > > a) guest account does not resolve the internal server error. The > > > > > > "linci" account was created via the method described in that > link you > > > > > > provided. Is it better I stick with the guest account? > > > > > > b) After changing the httpd.conf to match yours for this part, > the > > > > > > Apache services could not be restarted so I changed it back to > the > > > > > > original httpd.conf > > > > > > d) I am not sure how to do it, and am still figuring out the > right > > > > > > script to test (all the instruction provided online are mostly > for > > > > > > LINUX systems and I am using Win XP) > > > > > > However, I tested the script described in the first link and got > the > > > > > > following: > > > > > > XML Parsing Error: not well-formed > > > > > > Location: > http://localhost:8080/ISB/data/demo2009/tandem/test.pep.xml > > > > > > Line Number 1, Column 2:#!perl > > > > > > -^ > > > > > > > > Regards, > > > > > > Chris > > > > > > > > On Oct 28, 1:55 pm, Vishal Swaroop <vishal....@gmail.com> wrote: > > > > > > > > > Hi Chris, > > > > > > > > > Please clear thehttp://flic.kr/p/axzsk8anduploadfreshimage, > > > > sometimes > > > > > > > it is confusing on which step you are facing error.. > > > > > > > > > 1) Run this :http://localhost:<your port>/tpp-bin/check_env.pl and > > > > send > > > > > > > the details. > > > > > > > 2) Send your httpd.conf and apache latest log (under > > > > > > > C:\Apache...\logs\error.log), I will try to check. > > > > > > > 3) Send latest cmd_** file from c:\tmp > > > > > > > You can email me at vishal....@gmail.com or post here. > > > > > > > > > Other things.... > > > > > > > a) Have you tried with default user/ pwd (guest/guest) ? I am > not > > > > sure how > > > > > > > you have set the permission for user "linci", please > checkhttp:// > > > > tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial#Set... > > > > > > > > > b) Changing to my httpd.conf : Take back-up of your file and > try > > > > checking > > > > > > > "ScriptAlias" part as well as "Alias /tpp-bin > "C:/Inetpub/tpp-bin" > > > > > > > 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> > > > > > > > > > c) Restart Apache.... > > > > > > > > > d) Try running simple perl and cgi first that will ensure > apache is > > > > > > > configured correctly... you can get some samples on net. > > > >http://encodable.com/internal_server_error/ > > > > > > > > > Also, this might be of helphttp:// > > > > ask-leo.com/whats_an_internal_server_error_and_how_do_i_fix_it... > > > > > > > > > On Fri, Oct 28, 2011 at 3:57 PM, Chris L < > > > > linci%uci....@gtempaccount.com>wrote: > > > > > > > > > > Hi Vishal and all, > > > > > > > > I did a fresh install of TPP and Apache, but the 500 Internal > > > > Server > > > > > > > > Error still persists (http://flic.kr/p/axzsk8). The screen > shows > > > > up in > > > > > > > > every type of file I try to open inside my /demo2009 folder, > except > > > > > > > > for the .png picture files which I can view with no problem. > I > > > > have a > > > > > > > > bunch of cmd_ log files inside my C:/tmp folder, would you > like to > > > > see > > > > > > > > the contents? There are several differences between your > httpd.conf > > > > > > > > compared to mine, is it ok to manually change my httpd.conf > to > > > > match > > > > > > > > yours and would that help? Finally, how do you set > permission for > > > > cgi? > > > > > > > > Thank you for your help. > > > > > > > > > > Regards, > > > > > > > > Chris > > > > > > > > > > On Oct 26, 7:36 am, Vishal Swaroop <vishal....@gmail.com> > wrote: > > > > > > > > > Hi Chris, > > > > > > > > > > > a) It is good idea to do fresh install > > > > > > > > > b) TPP log file starts with "cmd_*", please other temporary > > > > directory or > > > > > > > > > search where it is created or may be check "TEMP" or "TMP" > > > > environment > > > > > > > > > variable under System and User Variable (Right click > > > > > > > > > Mycomputer>Properties>Advanced> Environment Variable).. > > > > > > > > > > > c) I believe your main issue is setting permission for > cgi.. > > > > > > > > > > > Here is my complete Apache httpd.conf ... > > > > > > > > > > > Let me know, I hope it will be fine.. > > > > > > > > > > > ------------------------HTTPD.CONF------------------------ > > > > > > > > > # > > > > > > > > > # This is the main Apache HTTP server configuration file. > It > > > > contains > > > > > > > > the > > > > > > > > > # configuration directives that give the server its > instructions. > > > > > > > > > # See <URL:http://httpd.apache.org/docs/2.2> for detailed > > > > information. > > > > > > > > > # In particular, see > > > > > > > > > # <URL: > http://httpd.apache.org/docs/2.2/mod/directives.html> > > > > > > > > > # for a discussion of each configuration directive. > > > > > > > > > # > > > > > > > > > # Do NOT simply read the instructions in here without > > > > understanding > > > > > > > > > # what they do. They're here only as hints or reminders. > If > > > > you are > > > > > > > > unsure > > > > > > > > > # consult the online docs. You have been warned. > > > > > > > > > # > > > > > > > > > # Configuration and logfile names: If the filenames you > specify > > > > for many > > > > > > > > > # of the server's control files begin with "/" (or > "drive:/" for > > > > Win32), > > > > > > > > the > > > > > > > > > # server will use that explicit path. If the filenames do > *not* > > > > begin > > > > > > > > > # with "/", the value of ServerRoot is prepended -- so > > > > "logs/foo.log" > > > > > > > > > # with ServerRoot set to "C:/Apache2.2" will be > interpreted by > > > > the > > > > > > > > > # server as "C:/Apache2.2/logs/foo.log". > > > > > > > > > # > > > > > > > > > # NOTE: Where filenames are specified, you must use forward > > > > slashes > > > > > > > > > # instead of backslashes (e.g., "c:/apache" instead of > > > > "c:\apache"). > > > > > > > > > # If a drive letter is omitted, the drive on which > httpd.exe is > > > > located > > > > > > > > > # will be used by default. It is recommended that you > always > > > > supply > > > > > > > > > # an explicit drive letter in absolute paths to avoid > confusion. > > > > > > > > > > > # > > > > > > > > > # ServerRoot: The top of the directory tree under which the > > > > server's > > > > > > > > > # configuration, error, and log files are kept. > > > > ... > > > > 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-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@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. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
