This came up before: http://groups.google.com/group/spctools-discuss/browse_thread/thread/fa8c50f53b35bc9a
although it's not clear if it was resolved. But you might have a look at the thread and see if it helps. On Mon, May 31, 2010 at 4:35 AM, Eliza <blond...@googlemail.com> wrote: > 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 <brian.pr...@insilicos.com> 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 <blond...@googlemail.com> 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 <brian.pr...@insilicos.com> 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 <vishal....@gmail.com> >> >> 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 <blond...@googlemail.com> 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 <vishal....@gmail.com> 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 >> >> >> > <brian.pr...@insilicos.com>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 <blond...@googlemail.com> >> >> >> > > 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 <brian.pr...@insilicos.com> >> >> >> > > > 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 <blond...@googlemail.com> >> >> >> > > >> 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. 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