OK so I was able to figure out how how to set the PATH for the webserver user and eradicated that error. That still leaves me with the following error in the browser:
Unable to access xml file via webserver, so cannot check xml file for changes () Check webserver configuration if desired. (URL: undefined) Suggestions on what I need to look at to fix this? On May 24, 7:39 pm, Brian Pratt <[email protected]> wrote: > PATH = /usr/local/bin:/usr/bin:/bin > > Doesn't seem to include your TPP executables. You'll need to figure > out how to update that for the Apache process user. > > On Mon, May 24, 2010 at 12:39 AM, Eliza <[email protected]> wrote: > > Here is the output (with some details removed) > > > SCRIPT_NAME = /tpp/cgi-bin/check_env.pl > > SERVER_NAME = servername > > SERVER_ADMIN = webmas...@localhost > > HTTP_ACCEPT_ENCODING = gzip,deflate > > HTTP_CONNECTION = keep-alive > > REQUEST_METHOD = GET > > HTTP_ACCEPT = text/html,application/xhtml+xml,application/xml;q=0.9,*/ > > *;q=0.8 > > SCRIPT_FILENAME = /usr/local/tpp/cgi-bin/check_env.pl > > SERVER_SOFTWARE = Apache/2.2.3 (Debian) PHP/5.2.0-8+etch16 > > HTTP_ACCEPT_CHARSET = ISO-8859-1,utf-8;q=0.7,*;q=0.7 > > QUERY_STRING = > > REMOTE_PORT = 3975 > > HTTP_USER_AGENT = Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv: > > 1.9.1.9) Gecko/20100315 Firefox/3.5.9 ( .NET CLR 3.5.30729) > > SERVER_PORT = 80 > > SERVER_SIGNATURE = > > Apache/2.2.3 (Debian) PHP/5.2.0-8+etch16 Server at server Port 80 > > > HTTP_ACCEPT_LANGUAGE = en-us,en;q=0.5 > > REMOTE_ADDR = xx.xx.xx.xx > > WEBSERVER_ROOT = /usr/local/tpp > > HTTP_KEEP_ALIVE = 300 > > SERVER_PROTOCOL = HTTP/1.1 > > PATH = /usr/local/bin:/usr/bin:/bin > > REQUEST_URI = /tpp/cgi-bin/check_env.pl > > GATEWAY_INTERFACE = CGI/1.1 > > SERVER_ADDR = 130.232.69.141 > > DOCUMENT_ROOT = /usr/local/tpp/html/ > > WEBSERVER_TMP = /usr/local/tpp/html/tmp > > HTTP_HOST = host > > > On May 21, 3:15 am, Brian Pratt <[email protected]> wrote: > >> PATH is of interest as well. Or you could just paste all the results > >> into a message to this list. > > >> On Thu, May 20, 2010 at 7:38 AM, Vishal Swaroop <[email protected]> > >> wrote: > >> > As I have not configured TPP on linux so I am not sure if I will be of > >> > help.... but check WEBSERVER_ROOT and SCRIPT_FILENAME = <path to > >> > tppbin>/check_env.pl > >> > See, if <path to tppbin> in SCRIPT_FILENAME is set in apache > >> > configuration > >> > file httpd.conf. > >> > As per your post description, does it mean that you are able to login and > >> > run some of the process from gui, on what event/ click you get this > >> > error, > >> > which browser you are using ? > >> > Thanks > >> > On Thu, May 20, 2010 at 4:42 AM, Eliza <[email protected]> wrote: > > >> >> The webserver is working fine, it is used to host a couple other sites > >> >> and they aren't experiencing any issues :-) > > >> >> I ran check_env.pl but I am not sure what I should which values I > >> >> should be verifying, can you provide any advice here? > > >> >> On May 19, 12:01 am, Vishal Swaroop <[email protected]> wrote: > >> >> > Hi Eliza, > > >> >> > Brian is right, it is difficult to debug through emails... > > >> >> > Though I have not configured it on linux but your issue seems to be > >> >> > related > >> >> > to environment setting (path for user, etc. as mentioned in 2nd. post) > > >> >> > - Check your apache httpd.conf file (should be somewhere under > >> >> > etc/apache...) and check if webserver is working (http://localhost) > >> >> > - You should also try checking > >> >> > http:///localhost/tpp/cgi-bin/check_env.pl , > >> >> > to check environment > > >> >> > Not sure if it will help but this is sample httpd.conf entry for > >> >> > webserver > >> >> > configured using cygwin... > > >> >> > ServerRoot "/usr" > >> >> > Listen 81 > >> >> > # > >> >> > # ISB-Tools Trans Proteomic Pipeline directive > >> >> > # > >> >> > ScriptLog /var/logs/apache2/cgi_log > >> >> > AddType text/html .shtml > >> >> > AddHandler server-parsed .shtml > >> >> > SetEnv WEBSERVER_ROOT /cygdrive/c/Inetpub/wwwroot/ > >> >> > SetEnv WEBSERVER_URLhttp://localhost:81/ > > >> >> > Alias /ISB/ "/cygdrive/c/Inetpub/wwwroot/ISB/" > >> >> > <Directory "/cygdrive/c/Inetpub/wwwroot/ISB/"> > >> >> > AllowOverride None > >> >> > Options Includes Indexes FollowSymLinks MultiViews > >> >> > Order allow,deny > >> >> > Allow from all > >> >> > </Directory> > > >> >> > Alias /tpp-bin/ "/cygdrive/c/Inetpub/tpp-bin/" > >> >> > <Directory "/cygdrive/c/Inetpub/tpp-bin/"> > >> >> > AllowOverride AuthConfig Limit > >> >> > Options ExecCGI Includes Indexes MultiViews > >> >> > AddHandler cgi-script .cgi .pl > >> >> > Order allow,deny > >> >> > Allow from all > >> >> > </Directory> > > >> >> > Thanks > >> >> > Vishal > > >> >> > On Tue, May 18, 2010 at 4:06 PM, Brian Pratt > >> >> > <[email protected]>wrote: > > >> >> > > I'm sorry you're having a hard time with it, but you just have to > >> >> > > get > >> >> > > in there and mess around with it, or find somebody locally who will > >> >> > > do > >> >> > > so for you. Getting a webserver configured on linux isn't trivial, > >> >> > > unfortunately, and not really the kind of thing that can be debugged > >> >> > > by email. > > >> >> > > Brian > > >> >> > > On Tue, May 18, 2010 at 6:52 AM, Eliza <[email protected]> > >> >> > > wrote: > >> >> > > > OK well this is a shame that no one seems to be able to help on > >> >> > > > this > >> >> > > > one. It seems to me this is more of a problem with the way the > >> >> > > > application is architected than a problem with the system I run it > >> >> > > > on. It's a bit of a shame that I don't feel I can support running > >> >> > > > TPP > >> >> > > > in a Linux environment. > > >> >> > > > On Mar 23, 6:23 pm, Brian Pratt <[email protected]> wrote: > >> >> > > >> Start with the "tpp_hostname: command not found" message. The > >> >> > > >> solution > >> >> > > is a > >> >> > > >> combination of setting the PATH for the webserver user, and > >> >> > > >> customizing > >> >> > > your > >> >> > > >> tpp_gui_config.pl file to tell the GUI where you installed the > >> >> > > >> various > >> >> > > >> executables. > > >> >> > > >> Good luck, > > >> >> > > >> Brian > > >> >> > > >> On Tue, Mar 23, 2010 at 6:20 AM, Eliza <[email protected]> > >> >> > > >> wrote: > >> >> > > >> > I posted the thread > > >> >> > > >> > >http://groups.google.com/group/spctools-discuss/browse_thread/thread/. > >> >> > > .. > >> >> > > >> > back in January but didn't receive any responses so I am asking > >> >> > > >> > again > >> >> > > >> > if anybody can assist. > > >> >> > > >> > When trying to use the TPP GUI the webserver error log is > >> >> > > >> > filled > >> >> > > >> > with > >> >> > > >> > the following error message: > > >> >> > > >> > [Fri Jan 08 14:01:42 2010] [error] [client xxx.xxx.xx.xx] sh: > >> >> > > >> > tpp_hostname: command not found, referer: > > >> >> > >http://localhost/tpp/cgi-bin/tpp_gui.pl?Action=display&page=filebrowser > > >> >> > > >> > I am also seeing the same error message in the GUI: > > >> >> > > >> > Unable to access xml file via webserver, so cannot check xml > >> >> > > >> > file > >> >> > > >> > for > >> >> > > >> > changes () > >> >> > > >> > Check webserver configuration if desired. > >> >> > > >> > (URL: undefined) > > >> >> > > >> > Debian Etch TPP version 4.3. Suggestions on how to fix this? > > >> >> > > >> > -- > >> >> > > >> > You received this message because you are subscribed to the > >> >> > > >> > Google > >> >> > > Groups > >> >> > > >> > "spctools-discuss" group. > >> >> > > >> > To post to this group, send email to > >> >> > > [email protected]. > >> >> > > >> > To unsubscribe from this group, send email to > > >> >> > > >> > [email protected]<spctools-discuss%[email protected]> > > >> >> > > <spctools-discuss%[email protected]<spctools-discuss%[email protected]> > > >> >> > > >> > . > >> >> > > >> > 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 > >> >> > > > [email protected]. > >> >> > > > To unsubscribe from this group, send email to > > >> >> > > [email protected]<spctools-discuss%[email protected]> > >> >> > > . > >> >> > > > 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 > >> >> > > [email protected]. > >> >> > > To unsubscribe from this group, send email to > > >> >> > > [email protected]<spctools-discuss%[email protected]> > >> >> > > . > >> >> > > 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 > >> >> > [email protected]. > >> >> > To unsubscribe from this group, send email to > >> >> > [email protected]. > >> >> > For more options, visit this group > >> >> > athttp://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 [email protected]. > >> >> To unsubscribe from this group, send email to > >> >> [email protected]. > >> >> 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 [email protected]. > >> > To unsubscribe from this group, send email to > >> > [email protected]. > >> > For more options, visit this group at > > ... > > read more » -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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