Hi Chris, OK.... I got the link... http://tools.proteomecenter.org/wiki/index.php?title=TPP_Demo2009
I will first try on my machine as I get time.. Thanks Vishal On Tue, Nov 1, 2011 at 8:41 PM, Vishal Swaroop <vishal....@gmail.com> wrote: > 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. 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