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

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

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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