Re: [spctools-discuss] TPP 4.6.2 installation problem Ubuntu 12.04 LTS virtual box

[Joseph Slagel]

Raj,

It sounds as if  you have an incorrect path somewhere in the configuration.  What are the contents of your Makefile.config.inc file?  And what did you use for paths in your  /etc/apache2/sites-available/tpp-x.y.z file?

-Joe

On Thu, Mar 21, 2013 at 6:19 AM, raju <rvmw...@gmail.com> wrote:

Hi,

I hope you can help.

I've been trying to install TPP on a linux vm, specifically Ubuntu 12.04 LTS in virtual box.

I've been following the TPP installation guide on http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3.

I've been copying and pasting where possible and it looked like everything was working during the setup i.e. no error messages.

However when i go to my web browser, google chrome, and go to http://localhost/tpp/cgi-bin/tpp_gui.pl

I get the following error:

----------------------------------------------------------------------------------------------------------------------

Not Found

The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this server.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

----------------------------------------------------------------------------------------------------------------------

Apache is working, as i can see the page.

I've checked port 80 is free

I've ensured the firewall has been disabled - just in case.

When I look in to the apache error log: 

The following errors were recorded:

----------------------------------------------------------------------------------------------------------------------

[Thu Mar 21 13:01:06 2013] [error] [client 127.0.0.1] File does not exist: /var/www/tpp

[Thu Mar 21 13:01:06 2013] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico

----------------------------------------------------------------------------------------------------------------------

I've checked that the file /etc/apache2/sites-available/tpp-x.y.z is as described in the installation guide

The file exists in the path stated and I copied and pasted the text into the file to avoid typos.

Any help would be greatly appreciated!!!

Many thanks,

Raj

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[Liam Bell]

Hi guys,

I am having a similar issue. Having followed the wiki instruction page and with the help of this forum successfully installing TPP on Linux 12.10 64bit. I completed the setting up apache instruction with no errors but I get a "The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this server." error when I attempt to go to http://localhost/tpp/cgi-bin/tpp_gui.pl.

My localhost is working (literally the message is "It works!". I have attempted to turn my firewall off but it makes no difference and I don't have any other services running through port 80. 

I have TPP sitting in /usr/local/tpp/ which houses directories for /bin, /cgi-bin, /data, /etc, /html, /schema.

I have gone through my Makefile.config.incl - below are my relevant settings:

TPP_ROOT=/usr/local/tpp/

TPP_WEB=/tpp/

And triple checked the paths that were set in the /etc/apache2/sites-available/tpp-4.6.2:

<VirtualHost *:80>

        # directory to store data for web browser viewing

        Alias /tpp/data "/usr/local/tpp/data"

        <Directory "/usr/local/tpp/data">

                AllowOverride None

                Options Indexes +FollowSymLinks Includes

                Order allow,deny

                Allow from all

        </Directory>

        # directory for tpp's html resources (css, js, images, etc)

        Alias /tpp/html "/usr/local/tpp/html"

        <Directory "/usr/local/tpp/html">

                AllowOverride None

                Options Includes Indexes FollowSymLinks MultiViews

                Order allow,deny

                Allow from all

        </Directory>

        # directory for tpp's schema resources

        <Directory "/usr/local/tpp/schema">

                AllowOverride None

                Options Includes Indexes FollowSymLinks MultiViews

                Order allow,deny

                Allow from all

        </Directory>

        # directory for tpp's executable files

        ScriptAlias /tpp/cgi-bin "/usr/local/tpp/cgi-bin"

        <Directory "/usr/local/tpp/cgi-bin">

                #AllowOverride AuthConfig Limit

                AllowOverride All

                Options Indexes +FollowSymLinks MultiViews ExecCGI +Includes

                AddHandler default-handler .jpg .png .css .ico .gif

                AddHandler cgi-script .cgi .pl

                Order allow,deny

                Allow from all

                SetEnv WEBSERVER_ROOT /usr/local/

Is it possible the above line should read /usr/local/tpp/ ???

                #SetEnv WEBSERVER_ROOT /var/www

        </Directory>

         

        # Enables Lorikeet spectrum display program to work for linux  

                Alias /ISB /usr/local/tpp

</VirtualHost>

[Liam Bell]

Hi guys,

I attempted the "fix" I thought might be the problem myself but it didn't make any difference.

The output from  sudo tail -f /var/log/apache2/error.log

Shows me:

[Fri Apr 19 14:01:38 2013] [error] [client 127.0.0.1] File does not exist: /var/www/tpp, referer: http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3

When I created an empty file /var/www/tpp I then got the error

[Fri Apr 19 14:03:15 2013] [error] [client 127.0.0.1] File does not exist: /var/www/tpp/cgi-bin/tpp_gui.pl, referer: http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3

If I then copy /usr/local/tpp/cgi-bin/tpp_gui.pl to /var/www/tpp/cgi-bin/tpp_gui.pl (and remove the empty tpp file I previously created) then I get the contents of thie tpp_gui.pl file displayed when I attempt I try to access http://localhost/tpp/cgi-bin/tpp_gui.pl on my browser. There is no error log file output for this though...

I hope somebody here can help me make sense of this?

Thanks,

Liam

[Ross]

Hi all,

I encountered this issue myself on Ubuntu 12.04: I found that making the tpp.4.6.2 file in /etc/apache2/sites-available didn't work either.

Instead, I found the following solved the issue:

• Paste the contents of the tpp-x.y.z file into /etc/apache2/httpd.conf
  

This definitely worked for me. I'm by no means an expert on Apache, however.

Hope this helps,

Ross

[Ross]

Bear in mind that in some httpd.conf files there is a dedicated section for this: ### Section 3: Virtual Hosts

[Liam Bell]

Hi Ross,

Thanks for the tip but it hasn't helped, would you be able to post the contents of your httpd.conf file for me so I can make sure it is the same as what I currently have?

Thanks,

Liam

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[Ross]

Hi Liam,

I'm sorry this hasn't helped. I've cross checked the TPP entries of our two httpd.conf files (the one you posted above) and they are identical. 

Alternatively it could be your permissions. For the entire /usr/local/tpp folder I have ownership set to apache (www-data) and permissions as drwxr-xr-x.

Does this help?

R

[Liam Bell]

It was set to root but I changed it to your settings and restarted apache but still not working...

It's rather vexing!

[Ross]

Hm. In your Makefile.config.incl, what is your PERL_LIB_CORE variable ? Does the version of Perl in that variable match the version installed on your computer? (command line: $ perl --version)

To test if the variable is viable, I navigated down the path of the variable in the terminal to see if the CORE folder actually existed. If I remember correctly I had to change the variable.

Let me know if that yields something, and I'll get on my TPP computer to find out what I did.

[Liam Bell]

Hi Ross,

Here you go:

PERL_LIB_CORE= /usr/lib/perl/5.10/CORE/

The CORE folder does exist at /usr/lib/perl/5.14.2/CORE.

Should I recompile and change that variable before I do?

[Ross]

Hi Liam,

I set mine to /usr/lib/perl/5.14/CORE, but using 5.14.2 shouldn't make a difference, since the 5.14 folder is a symlink to 5.14.2.

Yes, I would do that. Let's hope this is the fix.

[Liam Bell]

Nope - no dice...

Changed the PERL_LIB_CORE= /usr/lib/perl/15.4.2/CORE in the makefile.conf.incl file before re-running the compiling/building.

Ran through the rest fo the steps from http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3 as I have done successfully before.

The server is working still (localhost => It works!) but I can't load up http://localhost/tpp/cgi-bin/tpp_gui.pl - still getting "The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this server."

Any other ideas?

[Ross]

That's a shame. Did you completely remove all the old TPP files in between installs?

The only difference I can see between our installs at the moment, is that I removed the space in my variable assignment, between '=' and '/usr'...

What I will do is list all the things I did that were worth writing down (i.e. differed from the install guide...), and hope it helps:

Install pre-req that wasn't listed:

# apt-get install libgd2-xpm-dev

After install, when configuring Apache

# chown -R www-data:www-data /usr/local/tpp/

# chmod -R 711 /usr/local/tpp/

# chmod -R a+X /usr/local/tpp/

Does this help at all?

[Liam Bell]

I didn't remove the old files...not my brightest moment.

I will do that and then do a fresh clean install and make the mods you have made and let you know, although I may only be able to email the results tomorrow sometime.

Thank you for all your help though it's helping me NOT beat my head against a brick wall!

[Ross]

Having the old files remain might not make a difference, but intuitively removing them might help.

You're welcome, and good luck! 

[Jimmy Eng]

Liam,

At this point, perl is not the issue for you; our problem is definitely with your apache config.  The WEBSERVER_ROOT environment variable should point to your webserver's document root i.e. the directory that contains the index.html file that says "It Works!".  Is it possibly /var/www/html?  I can't imagine it being really /usr/local/ as you have in your apache2 config file for TPP below.  One step at a time so fix that first, restart apache, and try and to access http://localhost/tpp/cgi-bin/tpp_gui.pl.  If the page doesn't open, what is the error message in your apache error log file?

        # directory for tpp's executable files

        ScriptAlias /tpp/cgi-bin "/usr/local/tpp/cgi-bin"

        <Directory "/usr/local/tpp/cgi-bin">

                #AllowOverride AuthConfig Limit

                AllowOverride All

                Options Indexes +FollowSymLinks MultiViews ExecCGI +Includes

                AddHandler default-handler .jpg .png .css .ico .gif

                AddHandler cgi-script .cgi .pl

                Order allow,deny

                Allow from all

                SetEnv WEBSERVER_ROOT /usr/local/

Is it possible the above line should read /usr/local/tpp/ ???

                #SetEnv WEBSERVER_ROOT /var/www

        </Directory>

- Jimmy

[Liam Bell]

Hi Jimmy,

I looked up the WEBSERVER_ROOT environment variable in my /etc/apache2/apche2.conf file.

I think the relevant section is this:

# Global configuration

#

#

# ServerRoot: The top of the directory tree under which the server's

# configuration, error, and log files are kept.

#

# NOTE!  If you intend to place this on an NFS (or otherwise network)

# mounted filesystem then please read the LockFile documentation (available

# at <URL:http://httpd.apache.org/docs/2.2/mod/mpm_common.html#lockfile>);

# you will save yourself a lot of trouble.

#

# Do NOT add a slash at the end of the directory path.

#

#ServerRoot "/etc/apache2"

To which I edited so that,

ServerRoot "/var/www"

The index.html file you mentioned is located at /var/www/index.html

I then restarted apache and got the following:

liam@liam-Y500:~$ sudo /etc/init.d/apache2 restart

[sudo] password for liam: 

apache2: Syntax error on line 240 of /etc/apache2/apache2.conf: Include directory '/var/www/mods-enabled' not found

Action 'configtest' failed.

The Apache error log may have more information.

   ...fail!

What is going wrong? If I go to localhost in a web browser I still get "It works!".

--

[Liam Bell]

Trying to access the gui page I still get the same error message (404 Not found):

Not Found

The requested URL /tpp/cgi-bin/tpp_gui.pl was not found on this server.

Apache/2.2.22 (Ubuntu) Server at localhost Port 80

[Jimmy Eng]

Liam.

Your ServerRoot should probably still be "/etc/apache2".  ServerRoot is the root of the directory tree where your apache config files are kept.  What I was referring to was your DocumentRoot which is what your WEBSERVER_ROOT environment variable should be set to.  This DocumentRoot is the root directory where you serve your documents (i.e. index.html).

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[Liam Bell]

Where can I find what my WEBSERVER_ROOT variable has been set to? Which configuration file is it in?

[Jimmy Eng]

Liam,

Here's a snippet of what you posted 3 days ago.  The entry "SetEvn WEBSERVER_ROOT".  Set this to the same thing you have DocumentRoot set as in apache2.conf.

> On Thu, Apr 18, 2013 at 2:08 PM, Liam Bell <bell...@gmail.com> wrote:

And triple checked the paths that were set in the /etc/apache2/sites-available/tpp-4.6.2:

<VirtualHost *:80>

        # directory to store data for web browser viewing

        Alias /tpp/data "/usr/local/tpp/data"

        <Directory "/usr/local/tpp/data">

                AllowOverride None

                Options Indexes +FollowSymLinks Includes

                Order allow,deny

                Allow from all

        </Directory>

        # directory for tpp's html resources (css, js, images, etc)

        Alias /tpp/html "/usr/local/tpp/html"

        <Directory "/usr/local/tpp/html">

                AllowOverride None

                Options Includes Indexes FollowSymLinks MultiViews

                Order allow,deny

                Allow from all

        </Directory>

        # directory for tpp's schema resources

        <Directory "/usr/local/tpp/schema">

                AllowOverride None

                Options Includes Indexes FollowSymLinks MultiViews

                Order allow,deny

                Allow from all

        </Directory>

        # directory for tpp's executable files

        ScriptAlias /tpp/cgi-bin "/usr/local/tpp/cgi-bin"

        <Directory "/usr/local/tpp/cgi-bin">

                #AllowOverride AuthConfig Limit

                AllowOverride All

                Options Indexes +FollowSymLinks MultiViews ExecCGI +Includes

                AddHandler default-handler .jpg .png .css .ico .gif

                AddHandler cgi-script .cgi .pl

                Order allow,deny

                Allow from all

                SetEnv WEBSERVER_ROOT /usr/local/

Is it possible the above line should read /usr/local/tpp/ ???

                #SetEnv WEBSERVER_ROOT /var/www

        </Directory>

         

        # Enables Lorikeet spectrum display program to work for linux  

                Alias /ISB /usr/local/tpp

</VirtualHost>

[Liam Bell]

Hi Jimmy,

I set SetEnv WEBSERVER_ROOT /var/www in my /etc/apache2/sites-available/tpp-4.6.2

But when I checked for what my DocumentRoot variable was set to in my apache2.conf file but there was no variable for this set in that file. Where should this be set?

Thanks for your help so far, I appreciate it.

[Jimmy Eng]

Apache2 is a little foreign to me.  I've only setup one apache2/TPP server which I don't have easy access to in order to take a look.  See if this link helps you:

http://serverfault.com/questions/135993/how-do-i-change-the-document-root-of-a-linux-apache-server

[Liam Bell]

Hi guys,

I went back to the original installation guide and re-configured the apache part. However when I $ a2ensite tpp-4.6.2 I got the following output:

root@liam-Y500:~# a2ensite tpp-4.6.2

ERROR: Site tpp-4.6.2 not properly enabled: /etc/apache2/sites-enabled/tpp-4.6.2 is a real file, not touching it

I'm not sure what this means though. Busy looking into it and will give feedback when I have a clearer picture...

[Liam Bell]

Found the solution at http://forum.linode.com/viewtopic.php?t=7873, the second post by Piki sorted out the error whilst trying to enable to a2ensite command, however the site still does not load.

As far as I can tell my /etc/apache2/apache2.conf file is setup correctly, my /etc/apache2/sites-available/tpp-4.6.2 file is setup, my /var/www/ directory and my /usr/local/tpp/ directory is setup...I'm just not following what has gone wrong...?

[Jimmy Eng]

Liam,

I have to ask this basic question ... can you confirm you have /etc/apache2/sites-enabled/tpp-4.6.2?  Either as a direct copy of /etc/apache2/sites-available/tpp-4.6.2 or preferably as a symlink to /etc/apache2/sites-available/tpp-4.6.2?

What does your apache error log indicate when you try to open http://localhost/tpp/cgi-bin/tpp_gui.pl?

[tan42....@gmail.com]

Hey everyone,

it seems to me that I'm having a similar problem...
/etc/apache2/sites-enabled/tpp-4.6.2 is available as a symlink to /etc/apache2/sites-available/tpp-4.6.2

when I'm trying to go to http://localhost/tpp/cgi-bin/tpp_gui.pl there is the Error 404 not found, the apache error-log says the following line:
[error] [client ::1] File does not exist: /var/www/tpp

Thanks for any tipps on the issue!

[tan42....@gmail.com]

Setting
SetEnv WEBSERVER_ROOT /usr/local/ to SetEnv WEBSERVER_ROOT /usr/local/tpp/
did the job :)

[Joseph Slagel]

Glad you were able to figure it out.  Just to followup on this thread and let everyone know, since the 4.4.1 release of TPP I've been maintaining prebuilt Amazon AMIs for TPP .  (The latest 4.6.3 image is even built on Ubuntu 12.04 LTS).  Details about these images are available at:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_Amazon_Machine_Images

I also maintain a couple of bash scripts that are used to build said images.  These can be used as a reference for addressing some of the configuration issues that regularly come up.

http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/extern/hpctools/ec2/

And finally there is this slightly older set of instructions:

http://tools.proteomecenter.org/wiki/index.php?title=TPP_4.5.2:_Installing_on_Ubuntu_10.04.3

-Joe

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[Khader Shameer]

Hi


I have tried this but still getting a 404. When I load http://localhost/tpp/cgi-bin/tpp_gui.pl
Could you explain the steps you have done befor and after chaging the SetEnv ?

Thanks,
Shameer

[Anton Gurkov]

Hello!

The same issue for me as well. I have changed "SetEnv WEBSERVER_ROOT /usr/local/" to "SetEnv WEBSERVER_ROOT /usr/local/tpp/" in /etc/apache2/sites-enabled/tpp-4.6.3, but I have the same error.

Thanks for any response,

Anton.

вторник, 9 июля 2013 г., 7:19:05 UTC+9 пользователь Khader Shameer написал:

[Joseph Slagel]

Anton,

Can you take a look in your Apache httpd logs and see if there are any access or error messages occurring when you try to open TPP?

-Joe

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(206) 732-1362