Very odd that you were getting “Address is use” errors then..  What have you 
set the port to in your galaxy.ini file?

The missing index.html/index.php won’t make a difference to Galaxy, but it 
might prevent Apache from starting up.  I would put a simple index.html file, 
say:

<html><body><p>You should not see this.</p></body></html>

in /var/www/html just so Apache is happy and if you see that at least you will 
know Apache is up and running and listening on the correct ports. I would also 
forego the Apache rewrite rules until you know Galaxy is working.

Keith

> On Nov 3, 2015, at 12:15 PM, Makis Ladoukakis <makis4e...@hotmail.com> wrote:
> 
> Νο, no other service is running on 8081. This is the output of netstat -tulpn:
> 
> tcp        0      0 0.0.0.0:3306            0.0.0.0:*               LISTEN    
>   -
> tcp        0      0 0.0.0.0:22              0.0.0.0:*               LISTEN    
>   -
> tcp        0      0 127.0.0.1:25            0.0.0.0:*               LISTEN    
>   -
> tcp6       0      0 :::80                   :::*                    LISTEN    
>   -
> tcp6       0      0 :::22                   :::*                    LISTEN    
>   -
> tcp6       0      0 ::1:25                  :::*                    LISTEN    
>   -
> udp        0      0 0.0.0.0:123             0.0.0.0:*                         
>   -
> udp        0      0 127.0.0.1:323           0.0.0.0:*                         
>   -
> udp        0      0 0.0.0.0:5353            0.0.0.0:*                         
>   -
> udp        0      0 0.0.0.0:33715           0.0.0.0:*                         
>   -
> udp6       0      0 :::123                  :::*                              
>   -
> udp6       0      0 ::1:323                 :::*     
> 
> And no I only have an info.php in that directory. Does that affect Galaxy in 
> any way?
> 
> Thank you,
> Makis
> 
> Subject: Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused
> From: suder...@cs.vassar.edu <mailto:suder...@cs.vassar.edu>
> Date: Tue, 3 Nov 2015 12:07:12 -0500
> CC: federico.zambe...@gmail.com <mailto:federico.zambe...@gmail.com>; 
> galaxy-dev@lists.galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org>
> To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com>
> 
> Do you have another service running on 8081?  I see the server is complaining 
> about that address already being in use.  Also, do you have an index.html or 
> welcome.html in /var/www/html?
> 
> Cheers,
> Keith
> 
> On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis <makis4e...@hotmail.com 
> <mailto:makis4e...@hotmail.com>> wrote:
> 
> Hello,
> 
> Unfortunately I cannot change web servers at the moment. There are a lot of 
> applications that I would need to make changes for the nginx configuration 
> plus i am not very experienced with nginx (apparently not with apache as well 
> outside debian systems).
> 
> Thank you,
> Makis
> 
> > To: galaxy-dev@lists.galaxyproject.org 
> > <mailto:galaxy-dev@lists.galaxyproject.org>
> > From: federico.zambe...@gmail.com <mailto:federico.zambe...@gmail.com>
> > Date: Tue, 3 Nov 2015 17:19:59 +0100
> > Subject: Re: [galaxy-dev] FW: Galaxy on Centos via Apache - connection      
> > refused
> > 
> > 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 
> > > <mailto:david.trudg...@utsouthwestern.edu>
> > > To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com>; 
> > > jcsanch...@gmail.com <mailto:jcsanch...@gmail.com>
> > > CC: galaxy-...@lists.bx.psu.edu <mailto:galaxy-...@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 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 
> > > <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 <mailto:jcsanch...@gmail.com>>
> > > *Cc:* galaxy-...@lists.bx.psu.edu <mailto: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> 
> > > <mailto: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> 
> > > <mailto:galaxy-...@lists.bx.psu.edu <mailto:galaxy-...@lists.bx.psu.edu>>
> > > To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com> 
> > > <mailto: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>
> > > <mailto: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:
> > >
> > > <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: jcsanch...@gmail.com <mailto:jcsanch...@gmail.com> 
> > > <mailto:jcsanch...@gmail.com <mailto:jcsanch...@gmail.com>>
> > > To: makis4e...@hotmail.com <mailto:makis4e...@hotmail.com> 
> > > <mailto:makis4e...@hotmail.com <mailto:makis4e...@hotmail.com>>
> > > CC: galaxy-...@lists.bx.psu.edu <mailto:galaxy-...@lists.bx.psu.edu> 
> > > <mailto: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> 
> > > <mailto: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> 
> > > <mailto:makis4e...@hotmail.com <mailto:makis4e...@hotmail.com>>
> > > To: galaxy-dev@lists.galaxyproject.org 
> > > <mailto:galaxy-dev@lists.galaxyproject.org>
> > > <mailto: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 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 
> > > <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 <http://127.0.0.1:8081 <http://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 <http://185.25.151.159:39629 
> > > <http://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 <http://127.0.0.1:8081 <http://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 <http://147.102.86.121:51865 
> > > <http://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
> > >
> > >
> > >
> > > ___________________________________________________________
> > > 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/ <https://lists.galaxyproject.org/> To 
> > > search Galaxy mailing lists
> > > use the unified search at:
> > >  http://galaxyproject.org/search/mailinglists/ 
> > > <http://galaxyproject.org/search/mailinglists/>
> > >
> > >
> > > ___________________________________________________________
> > > 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/ <https://lists.galaxyproject.org/>
> > >
> > > To search Galaxy mailing lists use the unified search at:
> > >  http://galaxyproject.org/search/mailinglists/ 
> > > <http://galaxyproject.org/search/mailinglists/>
> > >
> > >
> > > ------------------------------------------------------------------------
> > >
> > > UTSouthwestern
> > >
> > > 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/ <https://lists.galaxyproject.org/>
> > >
> > > To search Galaxy mailing lists use the unified search at:
> > >  http://galaxyproject.org/search/mailinglists/ 
> > > <http://galaxyproject.org/search/mailinglists/>
> > >
> > 
> > ___________________________________________________________
> > 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/ <https://lists.galaxyproject.org/>
> > 
> > To search Galaxy mailing lists use the unified search at:
> >  http://galaxyproject.org/search/mailinglists/ 
> > <http://galaxyproject.org/search/mailinglists/>
> ___________________________________________________________
> 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:
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> 
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> <http://galaxyproject.org/search/mailinglists/>
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