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/axzsk8anduploadfresh image, > 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. > > > > > > # > > > > > > # Do not add a slash at the end of the directory path. If you > point > > > > > > # ServerRoot at a non-local disk, be sure to point the LockFile > directive > > > > > > # at a local disk. If you wish to share the same ServerRoot for > multiple > > > > > > # httpd daemons, you will need to change at least LockFile and > PidFile. > > > > > > # > > > > > > ServerRoot "C:/Apache2.2" > > > > > > > > # > > > > > > # Listen: Allows you to bind Apache to specific IP addresses > and/or > > > > > > # ports, instead of the default. See also the <VirtualHost> > > > > > > # directive. > > > > > > # > > > > > > # Change this to Listen on specific IP addresses as shown below > to > > > > > > # prevent Apache from glomming onto all bound IP addresses. > > > > > > # > > > > > > #Listen 12.34.56.78:80 > > > > > > Listen 81 > > > > > > > > # > > > > > > # Dynamic Shared Object (DSO) Support > > > > > > # > > > > > > # To be able to use the functionality of a module which was > built as a > > > > > DSO > > > > > > you > > > > > > # have to place corresponding `LoadModule' lines at this > location so the > > > > > > # directives contained in it are actually available _before_ > they are > > > > > used. > > > > > > # Statically compiled modules (those listed by `httpd -l') do > not need > > > > > > # to be loaded here. > > > > > > # > > > > > > # Example: > > > > > > # LoadModule foo_module modules/mod_foo.so > > > > > > # > > > > > > LoadModule actions_module modules/mod_actions.so > > > > > > LoadModule alias_module modules/mod_alias.so > > > > > > LoadModule asis_module modules/mod_asis.so > > > > > > LoadModule auth_basic_module modules/mod_auth_basic.so > > > > > > #LoadModule auth_digest_module modules/mod_auth_digest.so > > > > > > #LoadModule authn_alias_module modules/mod_authn_alias.so > > > > > > #LoadModule authn_anon_module modules/mod_authn_anon.so > > > > > > #LoadModule authn_dbd_module modules/mod_authn_dbd.so > > > > > > #LoadModule authn_dbm_module modules/mod_authn_dbm.so > > > > > > LoadModule authn_default_module modules/mod_authn_default.so > > > > > > LoadModule authn_file_module modules/mod_authn_file.so > > > > > > #LoadModule authnz_ldap_module modules/mod_authnz_ldap.so > > > > > > #LoadModule authz_dbm_module modules/mod_authz_dbm.so > > > > > > LoadModule authz_default_module modules/mod_authz_default.so > > > > > > LoadModule authz_groupfile_module modules/mod_authz_groupfile.so > > > > > > LoadModule authz_host_module modules/mod_authz_host.so > > > > > > #LoadModule authz_owner_module modules/mod_authz_owner.so > > > > > > LoadModule authz_user_module modules/mod_authz_user.so > > > > > > LoadModule autoindex_module modules/mod_autoindex.so > > > > > > #LoadModule cache_module modules/mod_cache.so > > > > > > #LoadModule cern_meta_module modules/mod_cern_meta.so > > > > > > LoadModule cgi_module modules/mod_cgi.so > > > > > > #LoadModule charset_lite_module modules/mod_charset_lite.so > > > > > > #LoadModule > > > > ... > > > > 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. 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