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%[email protected]> 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%[email protected]> wrote: > > > > > > > > > Hi Vishal and all, > > > Here is my check_env.pl > > SCRIPT_NAME = /tpp-bin/check_env.pl > > SERVER_NAME = localhost > > SERVER_ADMIN = [email protected] > > 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 <[email protected]> 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 [email protected] 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%[email protected]>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 <[email protected]> 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 » -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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