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 <[email protected]> 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%[email protected]>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%[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/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 [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
>
> ...
>
> read more »
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