Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-11-03 Thread Makis Ladoukakis 

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: makis4e...@hotmail.com
To: david.trudg...@utsouthwestern.edu; jcsanch...@gmail.com; plat...@platyna.org
Date: Tue, 3 Nov 2015 12:53:36 +0200
CC: galaxy-...@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 
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.trudg...@utsouthwestern.edu
To: makis4e...@hotmail.com; jcsanch...@gmail.com
CC: galaxy-...@lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused









SELinux policies are very strict on CentOS by default. Apache isn’t allowed to 
access files outside of its standard directories, nor
 access network resources. Your local Galaxy apps server is a network resource 
– even though it’s 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-boun...@lists.galaxyproject.org]
On Behalf Of Makis Ladoukakis

Sent: Friday, October 23, 2015 10:30 AM

To: Juan Carlos <jcsanch...@gmail.com>

Cc: galaxy-...@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 -

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-11-03 Thread Federico Zambelli 

Il 03/11/15 11:53, Makis Ladoukakis ha scritto:



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



Hello, I'm running a production Galaxy Server on CentOS and I can assure 
you it is perfectly feasible. But I'm using NGINX as a web server so I'm 
not able to help you with Apache configuration, sorry. Did you try to 
use NGINX instead of Apache in order to see if the problem is Apache 
related or system related?


Best,
Federico Z.






From: david.trudg...@utsouthwestern.edu
To: makis4e...@hotmail.com; jcsanch...@gmail.com
CC: galaxy-...@lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection
refused

SELinux policies are very strict on CentOS by default. Apache isn’t
allowed to access files outside of its standard directories, nor access
network resources. Your local Galaxy apps server is a network resource –
even though it’s 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-boun...@lists.galaxyproject.org]
*On Behalf Of *Makis Ladoukakis
*Sent:* Friday, October 23, 2015 10:30 AM
*To:* Juan Carlos <jcsanch...@gmail.com>
*Cc:* galaxy-...@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: jcsanch...@gmail.com <mailto:jcsanch...@gmail.com>
Date: Tue, 20 Oct 2015 22:25:00 +1030
CC: galaxy-...@lists.bx.psu.edu <mailto:galaxy-...@lists.bx.psu.edu>
To: makis4e...@hotmail.com <mailto:makis4e...@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 <makis4e...@hotmail.com
<mailto:makis4e...@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:


DirectoryIndex index.html welcome.html



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

---

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-11-03 Thread Makis Ladoukakis 
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 
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.trudg...@utsouthwestern.edu
To: makis4e...@hotmail.com; jcsanch...@gmail.com
CC: galaxy-...@lists.bx.psu.edu
Date: Fri, 23 Oct 2015 17:30:51 +
Subject: RE: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused









SELinux policies are very strict on CentOS by default. Apache isn’t allowed to 
access files outside of its standard directories, nor
 access network resources. Your local Galaxy apps server is a network resource 
– even though it’s 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-boun...@lists.galaxyproject.org]
On Behalf Of Makis Ladoukakis

Sent: Friday, October 23, 2015 10:30 AM

To: Juan Carlos <jcsanch...@gmail.com>

Cc: galaxy-...@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: jcsanch...@gmail.com

Date: Tue, 20 Oct 2015 22:25:00 +1030

CC: galaxy-...@lists.bx.psu.edu

To: makis4e...@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 <makis4e...@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-

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-10-23 Thread David Trudgian 
SELinux policies are very strict on CentOS by default. Apache isn't allowed to 
access files outside of its standard directories, nor access network resources. 
Your local Galaxy apps server is a network resource - even though it's 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-boun...@lists.galaxyproject.org] On Behalf 
Of Makis Ladoukakis
Sent: Friday, October 23, 2015 10:30 AM
To: Juan Carlos <jcsanch...@gmail.com>
Cc: galaxy-...@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: jcsanch...@gmail.com<mailto:jcsanch...@gmail.com>
Date: Tue, 20 Oct 2015 22:25:00 +1030
CC: galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu>
To: makis4e...@hotmail.com<mailto:makis4e...@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 
<makis4e...@hotmail.com<mailto:makis4e...@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:

DirectoryIndex index.html welcome.html


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: jcsanch...@gmail.com<mailto:jcsanch...@gmail.com>
To: makis4e...@hotmail.com<mailto:makis4e...@hotmail.com>
CC: galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@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 
<makis4e...@hotmail.com<mailto:makis4e...@hotmail.com>> wrote:
Forwading to this list too. I am not sure if they are two separate lists.

Makis

From: makis4e...@hotmail.com<mailto:makis4e...@hotmail.com>
To: 
galaxy-dev@lists.galaxyproject.org<mailto: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

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-10-23 Thread Zuzanna K. Filutowska 
It is because selinux policy is forbidding it to access the port. Solution - 
use semanage to allow this port to be used or disable selinux in 
/etc/sysconfig/selinux. 

-- 
Pozdrawiam,

Zuzanna K. Filutowska



W dniu 23 paź 2015, 17:30, o 17:30, użytkownik Makis Ladoukakis 
<makis4e...@hotmail.com> napisał:
>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: jcsanch...@gmail.com
>Date: Tue, 20 Oct 2015 22:25:00 +1030
>CC: galaxy-...@lists.bx.psu.edu
>To: makis4e...@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 <makis4e...@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:
>
>
>
>
>
>DirectoryIndex index.html welcome.html
>
>
>
>
>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: jcsanch...@gmail.com
>To: makis4e...@hotmail.com
>CC: galaxy-...@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?
>
>cheersjc
>On Tue, Oct 20, 2015 at 12:36 AM, Makis Ladoukakis
><makis4e...@hotmail.com> wrote:
>
>
>
>Forwading to this list too. I am not sure if they are two separate
>lists.
>
>Makis
>
>From: makis4e...@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_sty

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-10-20 Thread Makis Ladoukakis 
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:





DirectoryIndex index.html welcome.html




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: jcsanch...@gmail.com
To: makis4e...@hotmail.com
CC: galaxy-...@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?

cheersjc
On Tue, Oct 20, 2015 at 12:36 AM, Makis Ladoukakis <makis4e...@hotmail.com> 
wrote:



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

Makis

From: makis4e...@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 outpu

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-10-20 Thread Juan Carlos 

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 <makis4e...@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:
> 
> 
> DirectoryIndex index.html welcome.html
> 
> 
> 
> 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: jcsanch...@gmail.com
> To: makis4e...@hotmail.com
> CC: galaxy-...@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 <makis4e...@hotmail.com> 
> wrote:
> Forwading to this list too. I am not sure if they are two separate lists.
> 
> Makis
> 
> From: makis4e...@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 1

[galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-10-19 Thread Makis Ladoukakis 
Forwading to this list too. I am not sure if they are two separate lists.

Makis

From: makis4e...@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

Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection refused

2015-10-19 Thread Juan Carlos 
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 
wrote:

> Forwading to this list too. I am not sure if they are two separate lists.
>
> Makis
>
> --
> From: makis4e...@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