Also when I tried to run it without the addition of port 8081 in apache configuration file (when all I saw was a blank page) the error in /var/log/httpd/error_log was the following:

 AH01276: Cannot serve directory /var/www/html/: No matching DirectoryIndex (index.html,welcome.html,index.php) found, and server-generated directory index forbidden by Options directive



From: makis4ever@hotmail.com
To: david.trudgian@utsouthwestern.edu; jcsanchez2@gmail.com; platyna@platyna.org
Date: Tue, 3 Nov 2015 12:53:36 +0200
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

So I disabled SELinux

But that didn't make any difference. While the run.sh runs I still can't see anything but a blank page.

When I changed my apache configuration to include port 8081, the script didn't even run producing the error:


Traceback (most recent call last):
  File "./scripts/paster.py", line 32, in <module>
    serve.run()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 1052, in run
    invoke(command, command_name, options, args[1:])
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 1058, in invoke
    exit_code = runner.run(args)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 221, in run
    result = self.command()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 664, in command
    serve()
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/serve.py", line 648, in serve
    server(app)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 294, in server_wrapper
    **context.local_conf)
  File "/home/galaxy_test/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 99, in fix_call
    val = callable(*args, **kw)
  File "/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1342, in server_runner
    serve(wsgi_app, **kwargs)
  File "/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1291, in serve
    request_queue_size=request_queue_size)
  File "/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1134, in __init__
    request_queue_size=request_queue_size)
  File "/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1113, in __init__
    request_queue_size=request_queue_size)
  File "/home/galaxy_test/galaxy/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 328, in __init__
    HTTPServer.__init__(self, server_address, RequestHandlerClass)
  File "/usr/lib64/python2.7/SocketServer.py", line 419, in __init__
    self.server_bind()
  File "/usr/lib64/python2.7/BaseHTTPServer.py", line 108, in server_bind
    SocketServer.TCPServer.server_bind(self)
  File "/usr/lib64/python2.7/SocketServer.py", line 430, in server_bind
    self.socket.bind(self.server_address)
  File "/usr/lib64/python2.7/socket.py", line 224, in meth
    return getattr(self._sock,name)(*args)
socket.error: [Errno 98] Address already in use

That error was the same when I changed 80 to 8081 and when I added a second Listen with 8081.

Nothing seems to work on my server. Is Galaxy even compatible with CentOS? Is there something else that I am missing?

Any help would be appreciated. This installation seems impossible.

Thank you,
Makis





From: David.Trudgian@UTSouthwestern.edu
To: makis4ever@hotmail.com; jcsanchez2@gmail.com
CC: galaxy-dev@lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +0000
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

SELinux policies are very strict on CentOS by default. Apache isnt allowed to access files outside of its standard directories, nor access network resources. Your local Galaxy apps server is a network resource even though its local.

 

If you want to keep SELinux on then use audit2allow to see what policies will enable access:

 

cat /var/log/audit/audit.log | audit2allow v

 

Then you can use setsebool (temporary) and setsebool P (permanent) to enable.

 

 

--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833

 

From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Makis Ladoukakis
Sent: Friday, October 23, 2015 10:30 AM
To: Juan Carlos <jcsanchez2@gmail.com>
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

 

Hello,

That didn't work. The apache restart failed with the following error:

SELinux is preventing /usr/sbin/httpd from name_bind access on the tcp_socket port 8081.

Any idea why?

Kind regards,
Makis


Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused
From: jcsanchez2@gmail.com
Date: Tue, 20 Oct 2015 22:25:00 +1030
CC: galaxy-dev@lists.bx.psu.edu
To: makis4ever@hotmail.com

 

Hi,

If you have a line in your Apache conf like 

"Listen 80"

change to 

"Listen 8081"

 

 


On 20 Oct 2015, at 21:00, Makis Ladoukakis <makis4ever@hotmail.com> wrote:

Hello,

I am sorry but I have really no experience with setting up the Apache web server so I am not really sure how to do that. Can you please help me out with it? My apache configuration file is in /etc/httpd/conf/ directory and there are no directories such as /sites-available/ or /sites-enabled/ (as I would find in an ubuntu installation).

What I did already (after some advice from the server admin) is open up the 8081 port like that:

firewall-cmd  --permanent  --add-port=8081/tcp

firewall-cmd  --reload


and then I got another error:

 [cgi:error] [pid 29603] [client 115.230.124.164:4559] script not found or unable to stat: /var/www/cgi-bin/common

[autoindex:error] [pid 29716] [client 218.76.28.36:4468] AH01276: Cannot serve directory /var/www/html/: No matching DirectoryIndex (index.html,index.php) found, and server-generated directory index forbidden by Options directive


which I tried to solve by adding welcome.html as a recognizable filename in the apache configuration:

<IfModule dir_module>
DirectoryIndex index.html welcome.html
</IfModule>


but nothing worked and now the error_log shows the following:

[Tue Oct 20 13:15:23.719295 2015] [mpm_prefork:notice] [pid 29598] AH00170: caught SIGWINCH, shutting down gracefully
[Tue Oct 20 13:15:24.810684 2015] [core:notice] [pid 46896] SELinux policy enabled; httpd running as context system_u:system_r:httpd_t:s0
[Tue Oct 20 13:15:24.811647 2015] [suexec:notice] [pid 46896] AH01232: suEXEC mechanism enabled (wrapper: /usr/sbin/suexec)
[Tue Oct 20 13:15:24.846399 2015] [so:warn] [pid 46896] AH01574: module wsgi_module is already loaded, skipping
[Tue Oct 20 13:15:24.847316 2015] [auth_digest:notice] [pid 46896] AH01757: generating secret for digest authentication ...
[Tue Oct 20 13:15:24.848294 2015] [lbmethod_heartbeat:notice] [pid 46896] AH02282: No slotmem from mod_heartmonitor
[Tue Oct 20 13:15:24.870033 2015] [mpm_prefork:notice] [pid 46896] AH00163: Apache/2.4.6 (CentOS) PHP/5.4.16 mod_wsgi/3.4 Python/2.7.5 configured -- resuming normal operations
[Tue Oct 20 13:15:24.870075 2015] [core:notice] [pid 46896] AH00094: Command line: '/usr/sbin/httpd -D FOREGROUND'

And the webpage that galaxy is supposed to appear is still blank.

Any ideas?

Thank you,
Makis

 


Date: Tue, 20 Oct 2015 11:01:44 +1030
Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused
From: jcsanchez2@gmail.com
To: makis4ever@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu

hi,

 

Maybe sounds silly, but have you tried to put the apache configuration in a virtual host within the sites-enable site?

 

 

cheers

jc

 

On Tue, Oct 20, 2015 at 12:36 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:

Forwading to this list too. I am not sure if they are two separate lists.

Makis


From: makis4ever@hotmail.com
To: galaxy-dev@lists.galaxyproject.org
Date: Mon, 19 Oct 2015 17:04:13 +0300
Subject: [galaxy-dev] Galaxy on Centos via Apache - connection refused

 

Dear all,

I've been trying to set up a Galaxy instance on my CentOS server but even when I manage to run the simplest configuration correctly I can't seem to get it right on my browser as the connection is refused.

I have changed the host to 0.0.0.0, the port to 8081 and made the appropriate changes in Apache configuration file:

RewriteEngine on
RewriteRule ^/galaxy_test(.*) http://localhost:8081$1 [P]
RewriteRule ^/galaxy_test$ /galaxy_test/ [R]
RewriteRule ^/galaxy_test/static/style/(.*) /home/galaxy_test/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy_test/static/scripts/(.*) /home/galaxy_test/galaxy/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy_test/static/(.*) /home/galaxy_test/galaxy/static/$1 [L]
RewriteRule ^/galaxy_test/favicon.ico /home/galaxy_test/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy_test/robots.txt /home/galaxy_test/galaxy/static/robots.txt [L]

So when I tried to run it the first time I got the "temporarily out of service" error on my browser and the following error in apache log:

[Mon Oct 19 05:56:45.308714 2015] [proxy:error] [pid 18505] (13)Permission denied: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 05:56:45.308774 2015] [proxy_http:error] [pid 18505] [client 185.25.151.159:39629] AH01114: HTTP: failed to make connection to backend: localhost

Searching the internet I found the following solution:

/usr/sbin/setsebool httpd_can_network_connect 1
/usr/sbin/setsebool -P httpd_can_network_connect 1


but when I restarted my galaxy my browser would now show just a blank page and the error log of apache was:

[Mon Oct 19 15:29:09.425120 2015] [proxy:error] [pid 29699] (111)Connection refused: AH00957: HTTP: attempt to connect to 127.0.0.1:8081 (*) failed
[Mon Oct 19 15:29:09.425167 2015] [proxy_http:error] [pid 29699] [client 147.102.86.121:51865] AH01114: HTTP: failed to make connection to backend: localhost


Has anyone encountered that?

Kind regards,
Makis






P.S. In case that helps the output of iptables -L is the following:
Chain INPUT (policy ACCEPT)
target     prot opt source               destination        
ACCEPT     all  --  anywhere             anywhere             ctstate RELATED,ESTABLISHED
ACCEPT     all  --  anywhere             anywhere           
INPUT_direct  all  --  anywhere             anywhere           
INPUT_ZONES_SOURCE  all  --  anywhere             anywhere           
INPUT_ZONES  all  --  anywhere             anywhere           
ACCEPT     icmp --  anywhere             anywhere           
REJECT     all  --  anywhere             anywhere             reject-with icmp-host-prohibited

Chain FORWARD (policy ACCEPT)
target     prot opt source               destination        
ACCEPT     all  --  anywhere             anywhere             ctstate RELATED,ESTABLISHED
ACCEPT     all  --  anywhere             anywhere           
FORWARD_direct  all  --  anywhere             anywhere           
FORWARD_IN_ZONES_SOURCE  all  --  anywhere             anywhere           
FORWARD_IN_ZONES  all  --  anywhere             anywhere           
FORWARD_OUT_ZONES_SOURCE  all  --  anywhere             anywhere           
FORWARD_OUT_ZONES  all  --  anywhere             anywhere           
ACCEPT     icmp --  anywhere             anywhere           
REJECT     all  --  anywhere             anywhere             reject-with icmp-host-prohibited

Chain OUTPUT (policy ACCEPT)
target     prot opt source               destination        
OUTPUT_direct  all  --  anywhere             anywhere           

Chain FORWARD_IN_ZONES (1 references)
target     prot opt source               destination        
FWDI_public  all  --  anywhere             anywhere            [goto]
FWDI_public  all  --  anywhere             anywhere            [goto]

Chain FORWARD_IN_ZONES_SOURCE (1 references)
target     prot opt source               destination        

Chain FORWARD_OUT_ZONES (1 references)
target     prot opt source               destination        
FWDO_public  all  --  anywhere             anywhere            [goto]
FWDO_public  all  --  anywhere             anywhere            [goto]

Chain FORWARD_OUT_ZONES_SOURCE (1 references)
target     prot opt source               destination        

Chain FORWARD_direct (1 references)
target     prot opt source               destination        

Chain FWDI_public (2 references)
target     prot opt source               destination        
FWDI_public_log  all  --  anywhere             anywhere           
FWDI_public_deny  all  --  anywhere             anywhere           
FWDI_public_allow  all  --  anywhere             anywhere           

Chain FWDI_public_allow (1 references)
target     prot opt source               destination        

Chain FWDI_public_deny (1 references)
target     prot opt source               destination        

Chain FWDI_public_log (1 references)
target     prot opt source               destination        

Chain FWDO_public (2 references)
target     prot opt source               destination        
FWDO_public_log  all  --  anywhere             anywhere           
FWDO_public_deny  all  --  anywhere             anywhere           
FWDO_public_allow  all  --  anywhere             anywhere           

Chain FWDO_public_allow (1 references)
target     prot opt source               destination        

Chain FWDO_public_deny (1 references)
target     prot opt source               destination        

Chain FWDO_public_log (1 references)
target     prot opt source               destination        

Chain INPUT_ZONES (1 references)
target     prot opt source               destination        
IN_public  all  --  anywhere             anywhere            [goto]
IN_public  all  --  anywhere             anywhere            [goto]

Chain INPUT_ZONES_SOURCE (1 references)
target     prot opt source               destination        

Chain INPUT_direct (1 references)
target     prot opt source               destination        

Chain IN_public (2 references)
target     prot opt source               destination        
IN_public_log  all  --  anywhere             anywhere           
IN_public_deny  all  --  anywhere             anywhere           
IN_public_allow  all  --  anywhere             anywhere           

Chain IN_public_allow (1 references)
target     prot opt source               destination        
ACCEPT     tcp  --  anywhere             anywhere             tcp dpt:http ctstate NEW
ACCEPT     tcp  --  anywhere             anywhere             tcp dpt:ssh ctstate NEW
ACCEPT     tcp  --  anywhere             anywhere             tcp dpt:https ctstate NEW

Chain IN_public_deny (1 references)
target     prot opt source               destination        

Chain IN_public_log (1 references)
target     prot opt source               destination        

Chain OUTPUT_direct (1 references)
target     prot opt source               destination        



 

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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 



UT Southwestern

Medical Center

The future of medicine, today.


___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/