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/axzsk8and upload fresh 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 dav_module modules/mod_dav.so
> > > #LoadModule dav_fs_module modules/mod_dav_fs.so
> > > #LoadModule dav_lock_module modules/mod_dav_lock.so
> > > #LoadModule dbd_module modules/mod_dbd.so
> > > #LoadModule deflate_module modules/mod_deflate.so
> > > LoadModule dir_module modules/mod_dir.so
> > > #LoadModule disk_cache_module modules/mod_disk_cache.so
> > > #LoadModule dumpio_module modules/mod_dumpio.so
> > > LoadModule env_module modules/mod_env.so
> > > #LoadModule expires_module modules/mod_expires.so
> > > #LoadModule ext_filter_module modules/mod_ext_filter.so
> > > #LoadModule file_cache_module modules/mod_file_cache.so
> > > #LoadModule filter_module modules/mod_filter.so
> > > #LoadModule headers_module modules/mod_headers.so
> > > #LoadModule ident_module modules/mod_ident.so
> > > #LoadModule imagemap_module modules/mod_imagemap.so
> > > LoadModule include_module modules/mod_include.so
> > > #LoadModule info_module modules/mod_info.so
> > > LoadModule isapi_module modules/mod_isapi.so
> > > #LoadModule ldap_module modules/mod_ldap.so
> > > #LoadModule logio_module modules/mod_logio.so
> > > LoadModule log_config_module modules/mod_log_config.so
> > > #LoadModule log_forensic_module modules/mod_log_forensic.so
> > > #LoadModule mem_cache_module modules/mod_mem_cache.so
> > > LoadModule mime_module modules/mod_mime.so
> > > #LoadModule mime_magic_module modules/mod_mime_magic.so
> > > LoadModule negotiation_module modules/mod_negotiation.so
> > > #LoadModule proxy_module modules/mod_proxy.so
> > > #LoadModule proxy_ajp_module modules/mod_proxy_ajp.so
> > > #LoadModule proxy_balancer_module modules/mod_proxy_balancer.so
> > > #LoadModule proxy_connect_module modules/mod_proxy_connect.so
> > > #LoadModule proxy_ftp_module modules/mod_proxy_ftp.so
> > > #LoadModule proxy_http_module modules/mod_proxy_http.so
> > > #LoadModule reqtimeout_module modules/mod_reqtimeout.so
> > > #LoadModule rewrite_module modules/mod_rewrite.so
> > > LoadModule setenvif_module modules/mod_setenvif.so
> > > #LoadModule speling_module modules/mod_speling.so
> > > #LoadModule ssl_module modules/mod_ssl.so
> > > #LoadModule status_module modules/mod_status.so
> > > #LoadModule substitute_module modules/mod_substitute.so
> > > #LoadModule unique_id_module modules/mod_unique_id.so
> > > #LoadModule userdir_module modules/mod_userdir.so
> > > #LoadModule usertrack_module modules/mod_usertrack.so
> > > #LoadModule version_module modules/mod_version.so
> > > #LoadModule vhost_alias_module modules/mod_vhost_alias.so
>
> > > <IfModule !mpm_netware_module>
> > > <IfModule !mpm_winnt_module>
> > > #
> > > # If you wish httpd to run as a different user or group, you must run
> > > # httpd as root initially and it will switch.
> > > #
> > > # User/Group: The name (or #number) of the user/group to run httpd as.
> > > # It is usually good practice to create a dedicated user and group for
> > > # running httpd, as with most system services.
> > > #
> > > User daemon
> > > Group daemon
>
> > > </IfModule>
> > > </IfModule>
>
> > > # 'Main' server configuration
> > > #
> > > # The directives in this section set up the values used by the 'main'
> > > # server, which responds to any requests that aren't handled by a
> > > # <VirtualHost> definition.  These values also provide defaults
>
> ...
>
> read more »

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